"Hugo_Symbol" "Entrez_Gene_Id" "Center" "NCBI_Build" "Chromosome" "Start_Position" "End_Position" "Strand" "Variant_Classification" "Variant_Type" "Reference_Allele" "Tumor_Seq_Allele1" "Tumor_Seq_Allele2" "dbSNP_RS" "dbSNP_Val_Status" "Tumor_Sample_Barcode" "Matched_Norm_Sample_Barcode" "Match_Norm_Seq_Allele1" "Match_Norm_Seq_Allele2" "Tumor_Validation_Allele1" "Tumor_Validation_Allele2" "Match_Norm_Validation_Allele1" "Match_Norm_Validation_Allele2" "Verification_Status" "Validation_Status" "Mutation_Status" "Sequencing_Phase" "Sequence_Source" "Validation_Method" "Score" "BAM_File" "Sequencer" "Tumor_Sample_UUID" "Matched_Norm_Sample_UUID" "HGVSc" "HGVSp" "HGVSp_Short" "Transcript_ID" "Exon_Number" "t_depth" "t_ref_count" "t_alt_count" "n_depth" "n_ref_count" "n_alt_count" "all_effects" "Allele" "Gene" "Feature" "Feature_type" "One_Consequence" "Consequence" "cDNA_position" "CDS_position" "Protein_position" "Amino_acids" "Codons" "Existing_variation" "ALLELE_NUM" "DISTANCE" "TRANSCRIPT_STRAND" "SYMBOL" "SYMBOL_SOURCE" "HGNC_ID" "BIOTYPE" "CANONICAL" "CCDS" "ENSP" "SWISSPROT" "TREMBL" "UNIPARC" "RefSeq" "SIFT" "PolyPhen" "EXON" "INTRON" "DOMAINS" "GMAF" "AFR_MAF" "AMR_MAF" "ASN_MAF" "EAS_MAF" "EUR_MAF" "SAS_MAF" "AA_MAF" "EA_MAF" "CLIN_SIG" "SOMATIC" "PUBMED" "MOTIF_NAME" "MOTIF_POS" "HIGH_INF_POS" "MOTIF_SCORE_CHANGE" "IMPACT" "PICK" "VARIANT_CLASS" "TSL" "HGVS_OFFSET" "PHENO" "MINIMISED" "ExAC_AF" "ExAC_AF_Adj" "ExAC_AF_AFR" "ExAC_AF_AMR" "ExAC_AF_EAS" "ExAC_AF_FIN" "ExAC_AF_NFE" "ExAC_AF_OTH" "ExAC_AF_SAS" "GENE_PHENO" "FILTER" "CONTEXT" "src_vcf_id" "tumor_bam_uuid" "normal_bam_uuid" "case_id" "GDC_FILTER" "COSMIC" "MC3_Overlap" "GDC_Validation_Status"
"1" "PSMB2" 5690 "BI" "GRCh38" "chr1" 35631318 35631318 "+" "Missense_Mutation" "SNP" "C" "C" "T" "novel" NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.241G>A" "p.Ala81Thr" "p.A81T" "ENST00000373237" "3/6" 240 223 16 167 NA NA "PSMB2,missense_variant,p.A81T,ENST00000373237,NM_002794.4&NM_001199779.1,c.241G>A,MODERATE,YES,deleterious(0),probably_damaging(0.939),-1;PSMB2,5_prime_UTR_variant,,ENST00000621781,NM_001199780.1,c.-111G>A,MODIFIER,,,,-1;PSMB2,non_coding_transcript_exon_variant,,ENST00000630477,,n.129G>A,MODIFIER,,,,-1" "T" "ENSG00000126067" "ENST00000373237" "Transcript" "missense_variant" "missense_variant" "653/2701" "241/606" "81/201" "A/T" "Gct/Act" NA 1 NA -1 "PSMB2" "HGNC" "HGNC:9539" "protein_coding" "YES" "CCDS394.1" "ENSP00000362334" "P49721" NA "UPI0000111E4C" "NM_002794.4;NM_001199779.1" "deleterious(0)" "probably_damaging(0.939)" "3/6" NA "Pfam_domain:PF00227;Superfamily_domains:SSF56235" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "MODERATE" 1 "SNV" 1 NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "GTTAGCTGCTG" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" NA TRUE "Unknown"
"2" "CYP4A22" 284541 "BI" "GRCh38" "chr1" 47143887 47143887 "+" "Missense_Mutation" "SNP" "G" "G" "A" "rs536116490" "by1000G" "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.761G>A" "p.Arg254His" "p.R254H" "ENST00000371891" "6/12" 260 136 120 358 NA NA "CYP4A22,missense_variant,p.R254H,ENST00000371891,NM_001010969.2,c.761G>A,MODERATE,YES,tolerated(0.2),benign(0.013),1;CYP4A22,missense_variant,p.R254H,ENST00000620131,,c.761G>A,MODERATE,,tolerated(0.2),benign(0.012),1;CYP4A22,missense_variant,p.R254H,ENST00000294337,,c.761G>A,MODERATE,,tolerated(0.22),benign(0.013),1;CYP4A22,intron_variant,,ENST00000619754,,c.636-470G>A,MODIFIER,,,,1;CYP4A22,intron_variant,,ENST00000371890,,c.636-470G>A,MODIFIER,,,,1;CYP4A22-AS1,intron_variant,,ENST00000444042,,n.396+33148C>T,MODIFIER,YES,,,-1;CYP4A22,non_coding_transcript_exon_variant,,ENST00000485117,,n.812G>A,MODIFIER,,,,1;CYP4A22,intron_variant,,ENST00000490948,,n.687-470G>A,MODIFIER,,,,1" "A" "ENSG00000162365" "ENST00000371891" "Transcript" "missense_variant" "missense_variant" "792/2535" "761/1560" "254/519" "R/H" "cGc/cAc" "rs536116490" 1 NA 1 "CYP4A22" "HGNC" "HGNC:20575" "protein_coding" "YES" "CCDS30707.1" "ENSP00000360958" "Q5TCH4" NA "UPI00002371F0" "NM_001010969.2" "tolerated(0.2)" "benign(0.013)" "6/12" NA "Pfam_domain:PF00067;Superfamily_domains:SSF48264" 2e-04 0 0 NA 0.001 0 0 NA NA NA NA NA NA NA NA NA "MODERATE" 1 "SNV" 1 NA NA 1 4.118e-05 4.175e-05 0 0 0.0005782 0 0 0 0 NA "PASS" "ACACCGCGCCT" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "common_in_exac;wga_pair" NA TRUE "Unknown"
"3" "FUBP1" 8880 "BI" "GRCh38" "chr1" 77969945 77969945 "+" "Missense_Mutation" "SNP" "T" "T" "C" "novel" NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.191A>G" "p.Lys64Arg" "p.K64R" "ENST00000370768" "2/20" 69 37 32 109 NA NA "FUBP1,missense_variant,p.K64R,ENST00000370767,,c.191A>G,MODERATE,,deleterious(0),probably_damaging(0.983),-1;FUBP1,missense_variant,p.K64R,ENST00000370768,NM_003902.3,c.191A>G,MODERATE,YES,deleterious(0),probably_damaging(0.936),-1;FUBP1,missense_variant,p.K64R,ENST00000421641,,c.191A>G,MODERATE,,deleterious(0),probably_damaging(0.992),-1;FUBP1,missense_variant,p.K64R,ENST00000294623,,c.191A>G,MODERATE,,deleterious(0),probably_damaging(0.971),-1" "C" "ENSG00000162613" "ENST00000370768" "Transcript" "missense_variant" "missense_variant" "273/2378" "191/1935" "64/644" "K/R" "aAa/aGa" NA 1 NA -1 "FUBP1" "HGNC" "HGNC:4004" "protein_coding" "YES" "CCDS683.1" "ENSP00000359804" "Q96AE4" NA "UPI0000070218" "NM_003902.3" "deleterious(0)" "probably_damaging(0.936)" "2/20" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "MODERATE" 1 "SNV" 1 NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "GTCTTTTTTGT" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" NA TRUE "Unknown"
"4" "IGSF9" 57549 "BI" "GRCh38" "chr1" 159931229 159931229 "+" "Missense_Mutation" "SNP" "C" "C" "T" "rs771632078" "byFrequency" "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.1546G>A" "p.Val516Met" "p.V516M" "ENST00000368094" "13/21" 158 105 53 221 NA NA "IGSF9,missense_variant,p.V516M,ENST00000368094,NM_001135050.1,c.1546G>A,MODERATE,YES,deleterious(0),probably_damaging(0.995),-1;IGSF9,missense_variant,p.V500M,ENST00000361509,NM_020789.3,c.1498G>A,MODERATE,,deleterious(0),probably_damaging(0.992),-1;IGSF9,intron_variant,,ENST00000611023,,c.1345+600G>A,MODIFIER,,,,-1;IGSF9,non_coding_transcript_exon_variant,,ENST00000493195,,n.1573G>A,MODIFIER,,,,-1;IGSF9,non_coding_transcript_exon_variant,,ENST00000496645,,n.1050G>A,MODIFIER,,,,-1;IGSF9,intron_variant,,ENST00000476102,,n.1708+224G>A,MODIFIER,,,,-1" "T" "ENSG00000085552" "ENST00000368094" "Transcript" "missense_variant" "missense_variant" "1744/4044" "1546/3540" "516/1179" "V/M" "Gtg/Atg" "rs771632078" 1 NA -1 "IGSF9" "HGNC" "HGNC:18132" "protein_coding" "YES" "CCDS44254.1" "ENSP00000357073" "Q9P2J2" NA "UPI000004A10B" "NM_001135050.1" "deleterious(0)" "probably_damaging(0.995)" "13/21" NA "Pfam_domain:PF00041;PROSITE_profiles:PS50853;SMART_domains:SM00060;Superfamily_domains:SSF49265" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "MODERATE" 1 "SNV" 1 NA NA 1 2.471e-05 2.481e-05 0 8.688e-05 0 0.0001543 1.503e-05 0 0 NA "PASS" "CACCACGGACA" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" NA TRUE "Unknown"
"5" "PIGM" 93183 "BI" "GRCh38" "chr1" 160031244 160031244 "+" "Missense_Mutation" "SNP" "C" "C" "T" "novel" NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.496G>A" "p.Val166Ile" "p.V166I" "ENST00000368090" "1/1" 663 550 112 485 NA NA "PIGM,missense_variant,p.V166I,ENST00000368090,NM_145167.2,c.496G>A,MODERATE,YES,tolerated(0.55),benign(0.003),-1;RP11-226L15.5,upstream_gene_variant,,ENST00000562313,,,MODIFIER,YES,,,-1" "T" "ENSG00000143315" "ENST00000368090" "Transcript" "missense_variant" "missense_variant" "748/4319" "496/1272" "166/423" "V/I" "Gtc/Atc" NA 1 NA -1 "PIGM" "HGNC" "HGNC:18858" "protein_coding" "YES" "CCDS1192.1" "ENSP00000357069" "Q9H3S5" NA "UPI000006D9D7" "NM_145167.2" "tolerated(0.55)" "benign(0.003)" "1/1" NA "Pfam_domain:PF05007" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "MODERATE" 1 "SNV" NA NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "CGCGACGAGTC" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" NA TRUE "Unknown"
"6" "GPA33" 10223 "BI" "GRCh38" "chr1" 167054365 167054365 "+" "Missense_Mutation" "SNP" "C" "C" "T" "novel" NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.929G>A" "p.Gly310Glu" "p.G310E" "ENST00000367868" "7/7" 213 163 49 290 NA NA "GPA33,missense_variant,p.G310E,ENST00000367868,NM_005814.1,c.929G>A,MODERATE,YES,deleterious(0),probably_damaging(0.999),-1;RP11-102C16.3,intron_variant,,ENST00000417644,,n.216+1599C>T,MODIFIER,YES,,,1;GPA33,non_coding_transcript_exon_variant,,ENST00000527955,,n.1020G>A,MODIFIER,,,,-1" "T" "ENSG00000143167" "ENST00000367868" "Transcript" "missense_variant" "missense_variant" "1273/2802" "929/960" "310/319" "G/E" "gGg/gAg" NA 1 NA -1 "GPA33" "HGNC" "HGNC:4445" "protein_coding" "YES" "CCDS1258.1" "ENSP00000356842" "Q99795" NA "UPI000012502D" "NM_005814.1" "deleterious(0)" "probably_damaging(0.999)" "7/7" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "MODERATE" 1 "SNV" 1 NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "CACGCCCAGTG" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "gdc_pon;wga_pair" NA TRUE "Unknown"
"7" "RFWD2" 64326 "BI" "GRCh38" "chr1" 175947206 175947206 "+" "Missense_Mutation" "SNP" "C" "C" "A" "novel" NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.2167G>T" "p.Gly723Cys" "p.G723C" "ENST00000367669" "19/20" 320 271 49 297 NA NA "RFWD2,missense_variant,p.G723C,ENST00000367669,NM_001286644.1&NM_022457.6,c.2167G>T,MODERATE,YES,deleterious(0),probably_damaging(0.997),-1;RFWD2,missense_variant,p.G699C,ENST00000308769,NM_001001740.3,c.2095G>T,MODERATE,,deleterious(0),probably_damaging(0.999),-1;RFWD2,missense_variant,p.G558C,ENST00000367666,,c.1672G>T,MODERATE,,deleterious(0),probably_damaging(0.997),-1;RFWD2,3_prime_UTR_variant,,ENST00000367667,,c.*1343G>T,MODIFIER,,,,-1;RFWD2,non_coding_transcript_exon_variant,,ENST00000461830,,n.1780G>T,MODIFIER,,,,-1;RFWD2,non_coding_transcript_exon_variant,,ENST00000482305,,n.121G>T,MODIFIER,,,,-1" "A" "ENSG00000143207" "ENST00000367669" "Transcript" "missense_variant" "missense_variant" "2682/3033" "2167/2196" "723/731" "G/C" "Ggt/Tgt" NA 1 NA -1 "RFWD2" "HGNC" "HGNC:17440" "protein_coding" "YES" "CCDS30944.1" "ENSP00000356641" "Q8NHY2" NA "UPI0000061E51" "NM_001286644.1;NM_022457.6" "deleterious(0)" "probably_damaging(0.997)" "19/20" NA "Superfamily_domains:SSF50978" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "MODERATE" 1 "SNV" 1 NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "TGTACCCTGAC" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "gdc_pon;wga_pair" NA TRUE "Unknown"
"8" "CACNA1S" 779 "BI" "GRCh38" "chr1" 201092059 201092059 "+" "Missense_Mutation" "SNP" "T" "T" "C" "rs369332959" "byCluster;byFrequency" "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.454A>G" "p.Met152Val" "p.M152V" "ENST00000362061" "4/44" 66 45 21 53 NA NA "CACNA1S,missense_variant,p.M152V,ENST00000362061,NM_000069.2,c.454A>G,MODERATE,YES,tolerated_low_confidence(0.51),benign(0.004),-1;CACNA1S,missense_variant,p.M152V,ENST00000367338,,c.454A>G,MODERATE,,tolerated_low_confidence(0.48),benign(0.004),-1" "C" "ENSG00000081248" "ENST00000362061" "Transcript" "missense_variant" "missense_variant" "681/6166" "454/5622" "152/1873" "M/V" "Atg/Gtg" "rs369332959" 1 NA -1 "CACNA1S" "HGNC" "HGNC:1397" "protein_coding" "YES" "CCDS1407.1" "ENSP00000355192" "Q13698" NA "UPI000020471D" "NM_000069.2" "tolerated_low_confidence(0.51)" "benign(0.004)" "4/44" NA "Pfam_domain:PF00520;Superfamily_domains:SSF81324" NA NA NA NA NA NA NA 0 1e-04 NA NA NA NA NA NA NA "MODERATE" 1 "SNV" 1 NA NA 1 4.118e-05 4.119e-05 9.612e-05 0 0 0.0003024 1.499e-05 0 6.056e-05 NA "PASS" "GCTCATTGGGG" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" NA TRUE "Unknown"
"9" "C4BPA" 722 "BI" "GRCh38" "chr1" 207144684 207144684 "+" "Silent" "SNP" "C" "C" "T" "rs762923928" NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.1761C>T" "p.=" "p.S587S" "ENST00000367070" "12/12" 116 65 49 69 NA NA "C4BPA,synonymous_variant,p.S587S,ENST00000367070,NM_000715.3,c.1761C>T,LOW,YES,,,1" "T" "ENSG00000123838" "ENST00000367070" "Transcript" "synonymous_variant" "synonymous_variant" "1955/2243" "1761/1794" "587/597" "S" "agC/agT" "rs762923928" 1 NA 1 "C4BPA" "HGNC" "HGNC:1325" "protein_coding" "YES" "CCDS1477.1" "ENSP00000356037" "P04003" NA "UPI0000126C28" "NM_000715.3" NA NA "12/12" NA "Coiled-coils_(Ncoils):ncoils" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "LOW" 1 "SNV" 1 NA NA 1 8.238e-06 8.425e-06 0 8.811e-05 0 0 0 0 0 NA "PASS" "GACAGCGCAAG" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" NA TRUE "Unknown"
"10" "MARC2" 54996 "BI" "GRCh38" "chr1" 220761701 220761701 "+" "Missense_Mutation" "SNP" "G" "G" "A" "novel" NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.490G>A" "p.Ala164Thr" "p.A164T" "ENST00000366913" "3/8" 60 23 37 131 NA NA "MARC2,missense_variant,p.A164T,ENST00000366913,NM_017898.3,c.490G>A,MODERATE,YES,deleterious(0.03),possibly_damaging(0.699),1;MARC2,missense_variant,p.A164T,ENST00000359316,,c.490G>A,MODERATE,,deleterious(0.03),possibly_damaging(0.779),1;MARC2,missense_variant,p.A65T,ENST00000425560,,c.193G>A,MODERATE,,deleterious(0.03),possibly_damaging(0.699),1;MARC2,non_coding_transcript_exon_variant,,ENST00000496078,,n.189G>A,MODIFIER,,,,1" "A" "ENSG00000117791" "ENST00000366913" "Transcript" "missense_variant" "missense_variant" "688/2134" "490/1008" "164/335" "A/T" "Gca/Aca" NA 1 NA 1 "MARC2" "HGNC" "HGNC:26064" "protein_coding" "YES" "CCDS1525.1" "ENSP00000355880" "Q969Z3" NA NA "NM_017898.3" "deleterious(0.03)" "possibly_damaging(0.699)" "3/8" NA "Pfam_domain:PF03476;Superfamily_domains:SSF141673;Superfamily_domains:SSF50800" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "MODERATE" 1 "SNV" 1 NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "ATGAGGCAGCT" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" NA TRUE "Unknown"
"11" "NUP133" 55746 "BI" "GRCh38" "chr1" 229465422 229465422 "+" "Missense_Mutation" "SNP" "G" "G" "A" "rs537234819" "byCluster;byFrequency" "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.2297C>T" "p.Thr766Met" "p.T766M" "ENST00000261396" "17/26" 32 16 16 93 NA NA "NUP133,missense_variant,p.T766M,ENST00000261396,NM_018230.2,c.2297C>T,MODERATE,YES,tolerated(0.05),probably_damaging(0.996),-1" "A" "ENSG00000069248" "ENST00000261396" "Transcript" "missense_variant" "missense_variant;splice_region_variant" "2389/5207" "2297/3471" "766/1156" "T/M" "aCg/aTg" "rs537234819" 1 NA -1 "NUP133" "HGNC" "HGNC:18016" "protein_coding" "YES" "CCDS1579.1" "ENSP00000261396" "Q8WUM0" NA "UPI000013D17A" "NM_018230.2" "tolerated(0.05)" "probably_damaging(0.996)" "17/26" NA "Pfam_domain:PF03177" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "MODERATE" 1 "SNV" 1 NA NA 1 3.295e-05 3.298e-05 0 0 0 0 5.996e-05 0 0 NA "PASS" "TACCCGTCCAT" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" "COSM3418871" TRUE "Unknown"
"12" "NCOA1" 8648 "BI" "GRCh38" "chr2" 24705083 24705083 "+" "Splice_Region" "SNP" "C" "C" "T" "novel" NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.950-3C>T" NA NA "ENST00000348332" NA 201 171 30 379 NA NA "NCOA1,splice_region_variant,,ENST00000405141,,c.950-3C>T,LOW,,,,1;NCOA1,splice_region_variant,,ENST00000406961,,c.950-3C>T,LOW,YES,,,1;NCOA1,splice_region_variant,,ENST00000288599,NM_147223.2,c.950-3C>T,LOW,,,,1;NCOA1,splice_region_variant,,ENST00000348332,NM_003743.4,c.950-3C>T,LOW,,,,1;NCOA1,splice_region_variant,,ENST00000395856,NM_147233.2,c.950-3C>T,LOW,,,,1;NCOA1,splice_region_variant,,ENST00000407230,,c.497-3C>T,LOW,,,,1;NCOA1,upstream_gene_variant,,ENST00000486198,,,MODIFIER,,,,1" "T" "ENSG00000084676" "ENST00000348332" "Transcript" "splice_region_variant" "splice_region_variant;intron_variant" "-/6895" "-/4326" "-/1441" NA NA NA 1 NA 1 "NCOA1" "HGNC" "HGNC:7668" "protein_coding" NA "CCDS1712.1" "ENSP00000320940" "Q15788" NA "UPI000006E1F7" "NM_003743.4" NA NA NA "9/20" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "LOW" NA "SNV" 1 NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "TGAAACAGTGA" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "NonExonic;bitgt;wga_pair" NA TRUE "Unknown"
"13" "REV1" 51455 "BI" "GRCh38" "chr2" 99439145 99439145 "+" "Silent" "SNP" "G" "G" "A" "novel" NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.669C>T" "p.=" "p.A223A" "ENST00000258428" "6/23" 86 45 41 141 NA NA "REV1,synonymous_variant,p.A223A,ENST00000258428,NM_016316.2,c.669C>T,LOW,YES,,,-1;REV1,synonymous_variant,p.A223A,ENST00000393445,NM_001037872.1,c.669C>T,LOW,,,,-1;REV1,upstream_gene_variant,,ENST00000450415,,,MODIFIER,,,,-1;REV1,non_coding_transcript_exon_variant,,ENST00000465835,,n.624C>T,MODIFIER,,,,-1;REV1,upstream_gene_variant,,ENST00000486117,,,MODIFIER,,,,-1;REV1,upstream_gene_variant,,ENST00000482887,,,MODIFIER,,,,-1;REV1,3_prime_UTR_variant,,ENST00000413697,,c.*616C>T,MODIFIER,,,,-1;REV1,non_coding_transcript_exon_variant,,ENST00000473819,,n.781C>T,MODIFIER,,,,-1;REV1,upstream_gene_variant,,ENST00000491752,,,MODIFIER,,,,-1" "A" "ENSG00000135945" "ENST00000258428" "Transcript" "synonymous_variant" "synonymous_variant" "898/4751" "669/3756" "223/1251" "A" "gcC/gcT" NA 1 NA -1 "REV1" "HGNC" "HGNC:14060" "protein_coding" "YES" "CCDS2045.1" "ENSP00000258428" "Q9UBZ9" NA NA "NM_016316.2" NA NA "6/23" NA "PIRSF_domain:PIRSF036573" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "LOW" 1 "SNV" 1 NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "AAAATGGCAGT" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" NA TRUE "Unknown"
"14" "PAX3" 5077 "BI" "GRCh38" "chr2" 222220209 222220209 "+" "Silent" "SNP" "G" "G" "A" "novel" NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.1104C>T" "p.=" "p.D368D" "ENST00000350526" "7/8" 76 63 13 82 NA NA "PAX3,synonymous_variant,p.D368D,ENST00000350526,NM_181457.3,c.1104C>T,LOW,,,,-1;PAX3,synonymous_variant,p.D368D,ENST00000392069,NM_181459.3,c.1104C>T,LOW,YES,,,-1;PAX3,synonymous_variant,p.D368D,ENST00000344493,NM_181461.3,c.1104C>T,LOW,,,,-1;PAX3,synonymous_variant,p.D368D,ENST00000392070,NM_181458.3,c.1104C>T,LOW,,,,-1;PAX3,synonymous_variant,p.D368D,ENST00000336840,NM_181460.3,c.1104C>T,LOW,,,,-1;PAX3,synonymous_variant,p.D367D,ENST00000409551,NM_001127366.2,c.1101C>T,LOW,,,,-1;PAX3,non_coding_transcript_exon_variant,,ENST00000464706,,n.528C>T,MODIFIER,,,,-1;PAX3,non_coding_transcript_exon_variant,,ENST00000555548,,n.335C>T,MODIFIER,,,,-1" "A" "ENSG00000135903" "ENST00000350526" "Transcript" "synonymous_variant" "synonymous_variant" "1241/3610" "1104/1440" "368/479" "D" "gaC/gaT" NA 1 NA -1 "PAX3" "HGNC" "HGNC:8617" "protein_coding" NA "CCDS42826.1" "ENSP00000343052" "P23760" "A0A024R470" "UPI0000131369" "NM_181457.3" NA NA "7/8" NA "Pfam_domain:PF12360" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "LOW" NA "SNV" 5 NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "AAGCTGTCTGT" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" NA TRUE "Unknown"
"15" "ATP6V1A" 523 "BI" "GRCh38" "chr3" 113784410 113784410 "+" "Nonsense_Mutation" "SNP" "G" "G" "A" "novel" NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.398G>A" "p.Trp133Ter" "p.W133*" "ENST00000273398" "4/15" 147 137 10 266 NA NA "ATP6V1A,stop_gained,p.W133*,ENST00000273398,NM_001690.3,c.398G>A,HIGH,YES,,,1;ATP6V1A,stop_gained,p.W133*,ENST00000475322,,c.398G>A,HIGH,,,,1;ATP6V1A,stop_gained,p.W100*,ENST00000496747,,c.299G>A,HIGH,,,,1;ATP6V1A,3_prime_UTR_variant,,ENST00000470455,,c.*300G>A,MODIFIER,,,,1" "A" "ENSG00000114573" "ENST00000273398" "Transcript" "stop_gained" "stop_gained" "506/4591" "398/1854" "133/617" "W/*" "tGg/tAg" NA 1 NA 1 "ATP6V1A" "HGNC" "HGNC:851" "protein_coding" "YES" "CCDS2976.1" "ENSP00000273398" "P38606" NA "UPI000013809A" "NM_001690.3" NA NA "4/15" NA "TIGRFAM_domain:TIGR01042" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "HIGH" 1 "SNV" 1 NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "CAAATGGGACT" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" NA TRUE "Unknown"
"16" "RAB43" 339122 "BI" "GRCh38" "chr3" 129095009 129095009 "+" "Missense_Mutation" "SNP" "G" "G" "A" "novel" NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.365C>T" "p.Ser122Phe" "p.S122F" "ENST00000315150" "2/3" 242 203 38 297 NA NA "RAB43,missense_variant,p.S122F,ENST00000315150,NM_198490.2&NM_001204888.1,c.365C>T,MODERATE,YES,deleterious(0),probably_damaging(0.923),-1;RAB43,missense_variant,p.S122F,ENST00000393304,NM_001204886.1,c.365C>T,MODERATE,,deleterious(0),probably_damaging(0.923),-1;RAB43,missense_variant,p.S122F,ENST00000393305,NM_001204883.1,c.365C>T,MODERATE,,deleterious(0),probably_damaging(0.923),-1;RAB43,missense_variant,p.S122F,ENST00000393307,NM_001204884.1,c.365C>T,MODERATE,,deleterious(0),probably_damaging(0.923),-1;RAB43,missense_variant,p.S122F,ENST00000393308,NM_001204885.1,c.365C>T,MODERATE,,deleterious(0),probably_damaging(0.923),-1;RAB43,missense_variant,p.S122F,ENST00000476465,NM_001204887.1,c.365C>T,MODERATE,,deleterious(0.01),possibly_damaging(0.787),-1;RAB43,missense_variant,p.S122F,ENST00000615093,,c.365C>T,MODERATE,,deleterious(0.01),possibly_damaging(0.787),-1;ISY1-RAB43,3_prime_UTR_variant,,ENST00000418265,NM_001204890.1,c.*16C>T,MODIFIER,YES,,,-1;RAB43,downstream_gene_variant,,ENST00000457077,,,MODIFIER,,,,-1" "A" "ENSG00000172780" "ENST00000315150" "Transcript" "missense_variant" "missense_variant" "666/4467" "365/639" "122/212" "S/F" "tCc/tTc" NA 1 NA -1 "RAB43" "HGNC" "HGNC:19983" "protein_coding" "YES" "CCDS33850.1" "ENSP00000319781" "Q86YS6" NA "UPI000000D851" "NM_198490.2;NM_001204888.1" "deleterious(0)" "probably_damaging(0.923)" "2/3" NA "Pfam_domain:PF00071;Pfam_domain:PF08477;Pfam_domain:PF00025;Pfam_domain:PF00009;Prints_domain:PR00449;TIGRFAM_domain:TIGR00231;SMART_domains:SM00173;SMART_domains:SM00175;SMART_domains:SM00174;SMART_domains:SM00176;Superfamily_domains:SSF52540" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "MODERATE" 1 "SNV" 1 NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "TGTTGGAGCCC" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" NA TRUE "Unknown"
"17" "NAA11" 84779 "BI" "GRCh38" "chr4" 79325731 79325731 "+" "Silent" "SNP" "G" "G" "A" NA NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.147C>T" "p.=" "p.D49D" "ENST00000286794" "1/2" 57 38 19 15 NA NA "NAA11,synonymous_variant,p.D49D,ENST00000286794,NM_032693.2,c.147C>T,LOW,YES,,,-1;NAA11,upstream_gene_variant,,ENST00000513733,,,MODIFIER,,,,-1;NAA11,upstream_gene_variant,,ENST00000511542,,,MODIFIER,,,,-1" "A" "ENSG00000156269" "ENST00000286794" "Transcript" "synonymous_variant" "synonymous_variant" "320/2014" "147/690" "49/229" "D" "gaC/gaT" NA 1 NA -1 "NAA11" "HGNC" "HGNC:28125" "protein_coding" "YES" "CCDS47084.1" "ENSP00000286794" "Q9BSU3" NA "UPI00000467CA" "NM_032693.2" NA NA "1/2" NA "Pfam_domain:PF00583;PROSITE_profiles:PS51186;Superfamily_domains:SSF55729" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "LOW" 1 "SNV" 1 NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "TTCCCGTCCTC" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" "COSM1057992" TRUE "Unknown"
"18" "PDGFC" 56034 "BI" "GRCh38" "chr4" 156810917 156810917 "+" "Nonsense_Mutation" "SNP" "G" "G" "A" NA NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.415C>T" "p.Gln139Ter" "p.Q139*" "ENST00000502773" "3/6" 348 320 28 204 NA NA "PDGFC,stop_gained,p.Q139*,ENST00000502773,NM_016205.2,c.415C>T,HIGH,YES,,,-1;PDGFC,stop_gained,p.Q139*,ENST00000422544,,c.415C>T,HIGH,,,,-1;PDGFC,intron_variant,,ENST00000512711,,n.417+24998C>T,MODIFIER,,,,-1;PDGFC,upstream_gene_variant,,ENST00000511985,,,MODIFIER,,,,-1;PDGFC,3_prime_UTR_variant,,ENST00000274071,,c.*323C>T,MODIFIER,,,,-1;PDGFC,intron_variant,,ENST00000506880,,c.117+36C>T,MODIFIER,,,,-1" "A" "ENSG00000145431" "ENST00000502773" "Transcript" "stop_gained" "stop_gained" "906/4165" "415/1038" "139/345" "Q/*" "Caa/Taa" NA 1 NA -1 "PDGFC" "HGNC" "HGNC:8801" "protein_coding" "YES" "CCDS3795.1" "ENSP00000422464" "Q9NRA1" NA "UPI0000034814" "NM_016205.2" NA NA "3/6" NA "Pfam_domain:PF00431;PROSITE_profiles:PS01180;SMART_domains:SM00042;Superfamily_domains:SSF49854" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "HIGH" 1 "SNV" 1 NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "AATTTGATTTC" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" "COSM4493470" TRUE "Unknown"
"19" "LARS" 51520 "BI" "GRCh38" "chr5" 146128686 146128686 "+" "Missense_Mutation" "SNP" "G" "G" "A" "rs200546271" "byCluster;byFrequency" "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.2866C>T" "p.Arg956Cys" "p.R956C" "ENST00000394434" "27/32" 218 168 50 419 NA NA "LARS,missense_variant,p.R956C,ENST00000394434,NM_020117.9,c.2866C>T,MODERATE,YES,deleterious(0.01),benign(0.044),-1;LARS,missense_variant,p.R902C,ENST00000510191,,c.2704C>T,MODERATE,,deleterious(0.01),benign(0.044),-1;LARS,missense_variant,p.R265C,ENST00000274562,,c.793C>T,MODERATE,,deleterious(0),benign(0.044),-1;LARS,downstream_gene_variant,,ENST00000512412,,,MODIFIER,,,,-1;LARS,non_coding_transcript_exon_variant,,ENST00000506231,,n.2847C>T,MODIFIER,,,,-1;LARS,non_coding_transcript_exon_variant,,ENST00000508709,,n.400C>T,MODIFIER,,,,-1;LARS,downstream_gene_variant,,ENST00000504611,,,MODIFIER,,,,-1" "A" "ENSG00000133706" "ENST00000394434" "Transcript" "missense_variant" "missense_variant" "3033/4766" "2866/3531" "956/1176" "R/C" "Cgt/Tgt" "rs200546271" 1 NA -1 "LARS" "HGNC" "HGNC:6512" "protein_coding" "YES" "CCDS34265.1" "ENSP00000377954" "Q9P2J5" NA "UPI0000037316" "NM_020117.9" "deleterious(0.01)" "benign(0.044)" "27/32" NA "TIGRFAM_domain:TIGR00395;Superfamily_domains:SSF47323" NA NA NA NA NA NA NA 2e-04 0 NA NA NA NA NA NA NA "MODERATE" 1 "SNV" 1 NA NA 1 3.295e-05 3.299e-05 0.0002884 8.678e-05 0 0 0 0 0 NA "PASS" "TTTACGTAGAA" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" NA TRUE "Unknown"
"20" "NDST1" 3340 "BI" "GRCh38" "chr5" 150541579 150541579 "+" "Missense_Mutation" "SNP" "G" "G" "A" "novel" NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.1759G>A" "p.Glu587Lys" "p.E587K" "ENST00000261797" "9/15" 149 96 53 74 NA NA "NDST1,missense_variant,p.E587K,ENST00000261797,NM_001543.4,c.1759G>A,MODERATE,YES,tolerated(0.11),benign(0.281),1;NDST1,missense_variant,p.E587K,ENST00000523767,NM_001301063.1,c.1759G>A,MODERATE,,tolerated(0.06),benign(0.281),1" "A" "ENSG00000070614" "ENST00000261797" "Transcript" "missense_variant" "missense_variant" "2261/8030" "1759/2649" "587/882" "E/K" "Gag/Aag" NA 1 NA 1 "NDST1" "HGNC" "HGNC:7680" "protein_coding" "YES" "CCDS34277.1" "ENSP00000261797" "P52848" NA "UPI000012CDA5" "NM_001543.4" "tolerated(0.11)" "benign(0.281)" "9/15" NA "Superfamily_domains:SSF52540" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "MODERATE" 1 "SNV" 1 NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "CCTGCGAGGAC" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" NA TRUE "Unknown"
"21" "SH3PXD2B" 285590 "BI" "GRCh38" "chr5" 172339478 172339478 "+" "Missense_Mutation" "SNP" "G" "G" "C" "novel" NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.1627C>G" "p.Arg543Gly" "p.R543G" "ENST00000311601" "13/13" 42 32 10 83 NA NA "SH3PXD2B,missense_variant,p.R543G,ENST00000311601,NM_001017995.2,c.1627C>G,MODERATE,YES,tolerated(0.09),probably_damaging(0.955),-1;SH3PXD2B,intron_variant,,ENST00000519643,,c.1188+6658C>G,MODIFIER,,,,-1;SH3PXD2B,intron_variant,,ENST00000518522,,c.201-5709C>G,MODIFIER,,,,-1" "C" "ENSG00000174705" "ENST00000311601" "Transcript" "missense_variant" "missense_variant" "1798/7777" "1627/2736" "543/911" "R/G" "Cgg/Ggg" NA 1 NA -1 "SH3PXD2B" "HGNC" "HGNC:29242" "protein_coding" "YES" "CCDS34291.1" "ENSP00000309714" "A1X283" NA "UPI000020C12E" "NM_001017995.2" "tolerated(0.09)" "probably_damaging(0.955)" "13/13" NA "Low_complexity_(Seg):Seg" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "MODERATE" 1 "SNV" 1 NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "CTGCCGCTCCC" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" NA TRUE "Unknown"
"22" "ZNF318" 24149 "BI" "GRCh38" "chr6" 43357360 43357360 "+" "Silent" "SNP" "C" "C" "T" "novel" NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.954G>A" "p.=" "p.L318L" "ENST00000361428" "3/10" 389 292 95 189 NA NA "ZNF318,synonymous_variant,p.L318L,ENST00000361428,NM_014345.2,c.954G>A,LOW,YES,,,-1;ZNF318,synonymous_variant,p.L318L,ENST00000605935,,c.954G>A,LOW,,,,-1" "T" "ENSG00000171467" "ENST00000361428" "Transcript" "synonymous_variant" "synonymous_variant" "1032/8006" "954/6840" "318/2279" "L" "ctG/ctA" NA 1 NA -1 "ZNF318" "HGNC" "HGNC:13578" "protein_coding" "YES" "CCDS4895.2" "ENSP00000354964" "Q5VUA4" NA "UPI000049E044" "NM_014345.2" NA NA "3/10" NA "Low_complexity_(Seg):Seg;Coiled-coils_(Ncoils):ncoils" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "LOW" 1 "SNV" 1 NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "AGATCCAGTTC" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" NA TRUE "Unknown"
"23" "PGK2" 5232 "BI" "GRCh38" "chr6" 49786262 49786262 "+" "Missense_Mutation" "SNP" "G" "G" "A" "novel" NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.926C>T" "p.Pro309Leu" "p.P309L" "ENST00000304801" "1/1" 388 235 152 499 NA NA "PGK2,missense_variant,p.P309L,ENST00000304801,NM_138733.4,c.926C>T,MODERATE,YES,deleterious(0.02),benign(0.003),-1" "A" "ENSG00000170950" "ENST00000304801" "Transcript" "missense_variant" "missense_variant" "926/1254" "926/1254" "309/417" "P/L" "cCt/cTt" NA 1 NA -1 "PGK2" "HGNC" "HGNC:8898" "protein_coding" "YES" "CCDS4930.1" "ENSP00000305995" "P07205" NA NA "NM_138733.4" "deleterious(0.02)" "benign(0.003)" "1/1" NA "Pfam_domain:PF00162;Superfamily_domains:SSF53748" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "MODERATE" 1 "SNV" NA NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "AGCCAGGAGAT" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" NA TRUE "Unknown"
"24" "FAM83B" 222584 "BI" "GRCh38" "chr6" 54941728 54941728 "+" "Silent" "SNP" "G" "G" "A" "rs746397400" NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.2757G>A" "p.=" "p.T919T" "ENST00000306858" "5/5" 202 135 67 140 NA NA "FAM83B,synonymous_variant,p.T919T,ENST00000306858,NM_001010872.2,c.2757G>A,LOW,YES,,,1;RP3-523K23.2,upstream_gene_variant,,ENST00000562834,,,MODIFIER,YES,,,1" "A" "ENSG00000168143" "ENST00000306858" "Transcript" "synonymous_variant" "synonymous_variant" "2873/3167" "2757/3036" "919/1011" "T" "acG/acA" "rs746397400" 1 NA 1 "FAM83B" "HGNC" "HGNC:21357" "protein_coding" "YES" "CCDS34479.1" "ENSP00000304078" "Q5T0W9" NA "UPI00001D81EC" "NM_001010872.2" NA NA "5/5" NA "Low_complexity_(Seg):Seg" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "LOW" 1 "SNV" 1 NA NA 1 8.237e-06 8.256e-06 0 0 0 0 1.501e-05 0 0 NA "PASS" "CCAACGTCCAG" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" NA TRUE "Unknown"
"25" "COL12A1" 1303 "BI" "GRCh38" "chr6" 75090163 75090163 "+" "Missense_Mutation" "SNP" "C" "C" "T" "novel" NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.8888G>A" "p.Gly2963Glu" "p.G2963E" "ENST00000322507" "63/66" 130 87 43 196 NA NA "COL12A1,missense_variant,p.G2963E,ENST00000322507,NM_004370.5,c.8888G>A,MODERATE,YES,,probably_damaging(1),-1;COL12A1,missense_variant,p.G1774E,ENST00000615798,,c.5321G>A,MODERATE,,deleterious(0.01),probably_damaging(1),-1;COL12A1,missense_variant,p.G2959E,ENST00000483888,,c.8876G>A,MODERATE,,,probably_damaging(1),-1;COL12A1,missense_variant,p.G2887E,ENST00000416123,,c.8660G>A,MODERATE,,,probably_damaging(0.969),-1;COL12A1,missense_variant,p.G1799E,ENST00000345356,NM_080645.2,c.5396G>A,MODERATE,,deleterious(0.01),probably_damaging(1),-1;COL12A1,missense_variant,p.G601E,ENST00000425443,,c.1802G>A,MODERATE,,deleterious(0),probably_damaging(1),-1;COL12A1,non_coding_transcript_exon_variant,,ENST00000511023,,n.503G>A,MODIFIER,,,,-1" "T" "ENSG00000111799" "ENST00000322507" "Transcript" "missense_variant" "missense_variant" "9198/11723" "8888/9192" "2963/3063" "G/E" "gGg/gAg" NA 1 NA -1 "COL12A1" "HGNC" "HGNC:2188" "protein_coding" "YES" "CCDS43482.1" "ENSP00000325146" "Q99715" NA "UPI000045890B" "NM_004370.5" NA "probably_damaging(1)" "63/66" NA "Pfam_domain:PF01391;Low_complexity_(Seg):Seg;PROSITE_profiles:PS50315;PROSITE_profiles:PS50099" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "MODERATE" 1 "SNV" 1 NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "GCCGCCCCCCA" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" NA TRUE "Unknown"
"26" "POPDC3" 64208 "BI" "GRCh38" "chr6" 105159798 105159798 "+" "Silent" "SNP" "G" "G" "A" "rs774623615" NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.507C>T" "p.=" "p.G169G" "ENST00000254765" "3/4" 103 55 48 124 NA NA "POPDC3,synonymous_variant,p.G169G,ENST00000254765,NM_022361.4,c.507C>T,LOW,YES,,,-1;POPDC3,synonymous_variant,p.G15G,ENST00000429112,,c.45C>T,LOW,,,,-1;BVES-AS1,intron_variant,,ENST00000369122,,n.343-6746G>A,MODIFIER,YES,,,1;BVES-AS1,intron_variant,,ENST00000580511,,n.682+5307G>A,MODIFIER,,,,1;BVES-AS1,intron_variant,,ENST00000580854,,n.545+5307G>A,MODIFIER,,,,1;BVES-AS1,downstream_gene_variant,,ENST00000369120,,,MODIFIER,,,,1;POPDC3,non_coding_transcript_exon_variant,,ENST00000474760,,n.550C>T,MODIFIER,,,,-1;POPDC3,non_coding_transcript_exon_variant,,ENST00000489134,,n.486C>T,MODIFIER,,,,-1" "A" "ENSG00000132429" "ENST00000254765" "Transcript" "synonymous_variant" "synonymous_variant" "786/1345" "507/876" "169/291" "G" "ggC/ggT" "rs774623615" 1 NA -1 "POPDC3" "HGNC" "HGNC:17649" "protein_coding" "YES" "CCDS5052.1" "ENSP00000254765" "Q9HBV1" NA NA "NM_022361.4" NA NA "3/4" NA "Pfam_domain:PF04831;Superfamily_domains:SSF51206" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "LOW" 1 "SNV" 1 NA NA 1 8.236e-06 8.267e-06 0 0 0 0 1.503e-05 0 0 NA "PASS" "AATTCGCCATC" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" "COSM1439470" TRUE "Unknown"
"27" "THEMIS" 387357 "BI" "GRCh38" "chr6" 127812974 127812974 "+" "Missense_Mutation" "SNP" "C" "C" "T" "novel" NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.1667G>A" "p.Arg556His" "p.R556H" "ENST00000368248" "4/6" 260 208 52 145 NA NA "THEMIS,missense_variant,p.R556H,ENST00000368250,,c.1667G>A,MODERATE,YES,deleterious(0),possibly_damaging(0.828),-1;THEMIS,missense_variant,p.R556H,ENST00000368248,NM_001010923.2,c.1667G>A,MODERATE,,deleterious(0),possibly_damaging(0.828),-1;THEMIS,missense_variant,p.R521H,ENST00000537166,NM_001164687.1,c.1562G>A,MODERATE,,deleterious(0),possibly_damaging(0.828),-1;THEMIS,missense_variant,p.R477H,ENST00000626040,,c.1430G>A,MODERATE,,deleterious(0),possibly_damaging(0.828),-1;THEMIS,missense_variant,p.R556H,ENST00000630369,NM_001164685.1,c.1667G>A,MODERATE,,deleterious(0),possibly_damaging(0.897),-1;THEMIS,downstream_gene_variant,,ENST00000434358,,,MODIFIER,,,,-1" "T" "ENSG00000172673" "ENST00000368248" "Transcript" "missense_variant" "missense_variant" "1816/3866" "1667/1926" "556/641" "R/H" "cGc/cAc" NA 1 NA -1 "THEMIS" "HGNC" "HGNC:21569" "protein_coding" NA "CCDS34534.1" "ENSP00000357231" "Q8N1K5" NA "UPI00001C1E44" "NM_001010923.2" "deleterious(0)" "possibly_damaging(0.828)" "4/6" NA "Low_complexity_(Seg):Seg" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "MODERATE" NA "SNV" 1 NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "GAGGGCGAGGT" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "gdc_pon;wga_pair" NA TRUE "Unknown"
"28" "GRM1" 2911 "BI" "GRCh38" "chr6" 146434601 146434601 "+" "Silent" "SNP" "C" "C" "T" "novel" NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.3390C>T" "p.=" "p.D1130D" "ENST00000282753" "8/8" 201 150 49 115 NA NA "GRM1,synonymous_variant,p.D1130D,ENST00000361719,,c.3390C>T,LOW,YES,,,1;GRM1,synonymous_variant,p.D1130D,ENST00000282753,NM_001278064.1,c.3390C>T,LOW,,,,1;GRM1,3_prime_UTR_variant,,ENST00000492807,NM_001278066.1&NM_001278065.1,c.*754C>T,MODIFIER,,,,1;GRM1,3_prime_UTR_variant,,ENST00000355289,NM_001278067.1,c.*628C>T,MODIFIER,,,,1;GRM1,3_prime_UTR_variant,,ENST00000507907,,c.*719C>T,MODIFIER,,,,1" "T" "ENSG00000152822" "ENST00000282753" "Transcript" "synonymous_variant" "synonymous_variant" "3625/6622" "3390/3585" "1130/1194" "D" "gaC/gaT" NA 1 NA 1 "GRM1" "HGNC" "HGNC:4593" "protein_coding" NA "CCDS5209.1" "ENSP00000282753" "Q13255" NA "UPI000013DCFD" "NM_001278064.1" NA NA "8/8" NA "Low_complexity_(Seg):Seg;Coiled-coils_(Ncoils):ncoils" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "LOW" NA "SNV" 1 NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "GAGGACCTGCA" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" NA TRUE "Unknown"
"29" "IGFBP1" 3484 "BI" "GRCh38" "chr7" 45891962 45891962 "+" "Missense_Mutation" "SNP" "G" "G" "A" "rs146202574" "by1000G;byCluster" "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.550G>A" "p.Val184Ile" "p.V184I" "ENST00000275525" "3/4" 279 247 32 138 NA NA "IGFBP1,missense_variant,p.V184I,ENST00000275525,NM_000596.2,c.550G>A,MODERATE,YES,deleterious(0.01),benign(0.108),1;IGFBP1,missense_variant,p.V184I,ENST00000457280,,c.550G>A,MODERATE,,deleterious(0.01),benign(0.108),1;IGFBP1,intron_variant,,ENST00000468955,,c.520-998G>A,MODIFIER,,,,1" "A" "ENSG00000146678" "ENST00000275525" "Transcript" "missense_variant" "missense_variant" "846/1653" "550/780" "184/259" "V/I" "Gta/Ata" "rs146202574" 1 NA 1 "IGFBP1" "HGNC" "HGNC:5469" "protein_coding" "YES" "CCDS5504.1" "ENSP00000275525" "P08833" NA "UPI000012D10E" "NM_000596.2" "deleterious(0.01)" "benign(0.108)" "3/4" NA "Pfam_domain:PF00086;Prints_domain:PR01976;PROSITE_profiles:PS51162;Superfamily_domains:SSF57610" 2e-04 0 0 NA 0.001 0 0 7e-04 1e-04 NA NA NA NA NA NA NA "MODERATE" 1 "SNV" 1 NA NA 1 0.0001318 0.0001322 0.0005776 8.667e-05 0.000694 0 3.006e-05 0 6.102e-05 NA "PASS" "GAGTCGTAGAG" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "common_in_exac;wga_pair" "COSM3765352" TRUE "Unknown"
"30" "ZNF804B" 219578 "BI" "GRCh38" "chr7" 89334019 89334019 "+" "Missense_Mutation" "SNP" "G" "G" "T" "novel" NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.1037G>T" "p.Arg346Ile" "p.R346I" "ENST00000333190" "4/4" 52 24 28 124 NA NA "ZNF804B,missense_variant,p.R346I,ENST00000333190,NM_181646.2,c.1037G>T,MODERATE,YES,tolerated(0.06),possibly_damaging(0.774),1;ZNF804B,missense_variant,p.R263I,ENST00000611114,,c.788G>T,MODERATE,,deleterious(0.04),possibly_damaging(0.774),1" "T" "ENSG00000182348" "ENST00000333190" "Transcript" "missense_variant" "missense_variant" "1646/4659" "1037/4050" "346/1349" "R/I" "aGa/aTa" NA 1 NA 1 "ZNF804B" "HGNC" "HGNC:21958" "protein_coding" "YES" "CCDS5613.1" "ENSP00000329638" "A4D1E1" NA "UPI00001A92D2" "NM_181646.2" "tolerated(0.06)" "possibly_damaging(0.774)" "4/4" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "MODERATE" 1 "SNV" 1 NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "AACTAGAAATA" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" NA TRUE "Unknown"
"31" "PIK3CG" 5294 "BI" "GRCh38" "chr7" 106867647 106867647 "+" "Missense_Mutation" "SNP" "C" "C" "T" "novel" NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.86C>T" "p.Ala29Val" "p.A29V" "ENST00000359195" "2/11" 91 64 27 74 NA NA "PIK3CG,missense_variant,p.A29V,ENST00000359195,NM_002649.3,c.86C>T,MODERATE,YES,tolerated_low_confidence(0.22),benign(0.003),1;PIK3CG,missense_variant,p.A29V,ENST00000496166,NM_001282426.1,c.86C>T,MODERATE,,tolerated_low_confidence(0.22),benign(0.003),1;PIK3CG,missense_variant,p.A29V,ENST00000440650,NM_001282427.1,c.86C>T,MODERATE,,tolerated_low_confidence(0.22),benign(0.003),1;PIK3CG,intron_variant,,ENST00000473541,,c.-187+2221C>T,MODIFIER,,,,1" "T" "ENSG00000105851" "ENST00000359195" "Transcript" "missense_variant" "missense_variant" "396/5377" "86/3309" "29/1102" "A/V" "gCg/gTg" NA 1 NA 1 "PIK3CG" "HGNC" "HGNC:8978" "protein_coding" "YES" "CCDS5739.1" "ENSP00000352121" "P48736" "A0A024R720" "UPI00000746B8" "NM_002649.3" "tolerated_low_confidence(0.22)" "benign(0.003)" "2/11" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "MODERATE" 1 "SNV" 1 NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "TGCTGCGGCCA" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" NA TRUE "Unknown"
"32" "FLNC" 2318 "BI" "GRCh38" "chr7" 128849444 128849444 "+" "Missense_Mutation" "SNP" "G" "G" "A" "novel" NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.5065G>A" "p.Glu1689Lys" "p.E1689K" "ENST00000325888" "30/48" 163 120 43 130 NA NA "FLNC,missense_variant,p.E1689K,ENST00000325888,NM_001458.4,c.5065G>A,MODERATE,YES,tolerated(0.05),probably_damaging(0.999),1;FLNC,missense_variant,p.E1689K,ENST00000346177,NM_001127487.1,c.5065G>A,MODERATE,,tolerated(0.06),probably_damaging(0.998),1;RP11-309L24.2,downstream_gene_variant,,ENST00000469965,,,MODIFIER,YES,,,-1" "A" "ENSG00000128591" "ENST00000325888" "Transcript" "missense_variant" "missense_variant" "5326/9188" "5065/8178" "1689/2725" "E/K" "Gag/Aag" NA 1 NA 1 "FLNC" "HGNC" "HGNC:3756" "protein_coding" "YES" "CCDS43644.1" "ENSP00000327145" "Q14315" NA "UPI000006DE6D" "NM_001458.4" "tolerated(0.05)" "probably_damaging(0.999)" "30/48" NA "Pfam_domain:PF00630;PROSITE_profiles:PS50194;SMART_domains:SM00557;Superfamily_domains:SSF81296" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "MODERATE" 1 "SNV" 1 NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "GGGCAGAGCTC" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" NA TRUE "Unknown"
"33" "FLNC" 2318 "BI" "GRCh38" "chr7" 128849465 128849465 "+" "Missense_Mutation" "SNP" "G" "G" "A" "novel" NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.5086G>A" "p.Glu1696Lys" "p.E1696K" "ENST00000325888" "30/48" 154 109 45 136 NA NA "FLNC,missense_variant,p.E1696K,ENST00000325888,NM_001458.4,c.5086G>A,MODERATE,YES,deleterious(0.03),probably_damaging(0.999),1;FLNC,missense_variant,p.E1696K,ENST00000346177,NM_001127487.1,c.5086G>A,MODERATE,,deleterious(0.04),probably_damaging(0.998),1;RP11-309L24.2,downstream_gene_variant,,ENST00000469965,,,MODIFIER,YES,,,-1" "A" "ENSG00000128591" "ENST00000325888" "Transcript" "missense_variant" "missense_variant" "5347/9188" "5086/8178" "1696/2725" "E/K" "Gag/Aag" NA 1 NA 1 "FLNC" "HGNC" "HGNC:3756" "protein_coding" "YES" "CCDS43644.1" "ENSP00000327145" "Q14315" NA "UPI000006DE6D" "NM_001458.4" "deleterious(0.03)" "probably_damaging(0.999)" "30/48" NA "Pfam_domain:PF00630;PROSITE_profiles:PS50194;SMART_domains:SM00557;Superfamily_domains:SSF81296" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "MODERATE" 1 "SNV" 1 NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "TGGTTGAGAAC" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" NA TRUE "Unknown"
"34" "TRPV6" 55503 "BI" "GRCh38" "chr7" 142875133 142875133 "+" "Missense_Mutation" "SNP" "C" "C" "T" NA NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.1154G>A" "p.Arg385Gln" "p.R385Q" "ENST00000359396" "9/15" 92 84 8 75 NA NA "TRPV6,missense_variant,p.R256Q,ENST00000463646,,c.767G>A,MODERATE,,deleterious(0.04),probably_damaging(0.987),-1;TRPV6,missense_variant,p.R385Q,ENST00000359396,NM_018646.4,c.1154G>A,MODERATE,YES,deleterious(0.04),probably_damaging(0.991),-1;TRPV6,missense_variant,p.R8Q,ENST00000436401,,c.23G>A,MODERATE,,deleterious(0.04),probably_damaging(0.991),-1;EPHB6,downstream_gene_variant,,ENST00000619012,,,MODIFIER,YES,,,1;EPHB6,downstream_gene_variant,,ENST00000422643,NM_004445.4,,MODIFIER,,,,1;EPHB6,downstream_gene_variant,,ENST00000411471,NM_001280795.1&NM_001280794.1,,MODIFIER,,,,1;EPHB6,downstream_gene_variant,,ENST00000476059,,,MODIFIER,,,,1;TRPV6,downstream_gene_variant,,ENST00000431833,,,MODIFIER,,,,-1;RP11-114L10.2,upstream_gene_variant,,ENST00000438839,,,MODIFIER,YES,,,1;EPHB6,downstream_gene_variant,,ENST00000617632,,,MODIFIER,,,,1;TRPV6,non_coding_transcript_exon_variant,,ENST00000615386,,n.8915G>A,MODIFIER,,,,-1;TRPV6,non_coding_transcript_exon_variant,,ENST00000485138,,n.525G>A,MODIFIER,,,,-1;TRPV6,non_coding_transcript_exon_variant,,ENST00000619250,,n.932G>A,MODIFIER,,,,-1;EPHB6,downstream_gene_variant,,ENST00000616380,,,MODIFIER,,,,1;EPHB6,downstream_gene_variant,,ENST00000614832,,,MODIFIER,,,,1;EPHB6,downstream_gene_variant,,ENST00000611578,,,MODIFIER,,,,1;EPHB6,downstream_gene_variant,,ENST00000486511,,,MODIFIER,,,,1;TRPV6,downstream_gene_variant,,ENST00000489123,,,MODIFIER,,,,-1;TRPV6,downstream_gene_variant,,ENST00000474388,,,MODIFIER,,,,-1;EPHB6,downstream_gene_variant,,ENST00000471581,,,MODIFIER,,,,1" "T" "ENSG00000165125" "ENST00000359396" "Transcript" "missense_variant" "missense_variant" "1400/2928" "1154/2178" "385/725" "R/Q" "cGg/cAg" NA 1 NA -1 "TRPV6" "HGNC" "HGNC:14006" "protein_coding" "YES" "CCDS5874.1" "ENSP00000352358" "Q9H1D0" NA "UPI000000D91B" "NM_018646.4" "deleterious(0.04)" "probably_damaging(0.991)" "9/15" NA "TIGRFAM_domain:TIGR00870" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "MODERATE" 1 "SNV" 1 NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "CCAGCCGGATA" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" "COSM1448775" TRUE "Unknown"
"35" "PTPRN2" 5799 "BI" "GRCh38" "chr7" 158316864 158316864 "+" "Missense_Mutation" "SNP" "C" "C" "A" "novel" NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.232G>T" "p.Ala78Ser" "p.A78S" "ENST00000389418" "3/23" 136 119 17 85 NA NA "PTPRN2,missense_variant,p.A78S,ENST00000389413,NM_130843.2,c.232G>T,MODERATE,,deleterious(0.03),benign(0.359),-1;PTPRN2,missense_variant,p.A78S,ENST00000389418,NM_002847.3,c.232G>T,MODERATE,YES,deleterious(0.04),benign(0.196),-1;PTPRN2,missense_variant,p.A61S,ENST00000389416,NM_130842.2,c.181G>T,MODERATE,,tolerated(0.09),benign(0.15),-1;PTPRN2,intron_variant,,ENST00000409483,,c.164-111591G>T,MODIFIER,,,,-1" "A" "ENSG00000155093" "ENST00000389418" "Transcript" "missense_variant" "missense_variant" "242/4706" "232/3048" "78/1015" "A/S" "Gcc/Tcc" NA 1 NA -1 "PTPRN2" "HGNC" "HGNC:9677" "protein_coding" "YES" "CCDS5947.1" "ENSP00000374069" "Q92932" NA "UPI000002E7C7" "NM_002847.3" "deleterious(0.04)" "benign(0.196)" "3/23" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "MODERATE" 1 "SNV" 1 NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "CAGGGCCACGG" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" NA TRUE "Unknown"
"36" "ZMAT4" 79698 "BI" "GRCh38" "chr8" 40697297 40697297 "+" "Silent" "SNP" "G" "G" "A" "rs189553545" "by1000G;byCluster;byFrequency" "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.297C>T" "p.=" "p.H99H" "ENST00000297737" "4/7" 680 301 378 252 NA NA "ZMAT4,synonymous_variant,p.H99H,ENST00000297737,NM_024645.2,c.297C>T,LOW,YES,,,-1;ZMAT4,synonymous_variant,p.H99H,ENST00000315769,NM_001135731.1,c.297C>T,LOW,,,,-1;ZMAT4,synonymous_variant,p.H99H,ENST00000519406,,c.297C>T,LOW,,,,-1;ZMAT4,3_prime_UTR_variant,,ENST00000523188,,c.*205C>T,MODIFIER,,,,-1;ZMAT4,3_prime_UTR_variant,,ENST00000523542,,c.*219C>T,MODIFIER,,,,-1;ZMAT4,non_coding_transcript_exon_variant,,ENST00000519806,,n.41C>T,MODIFIER,,,,-1;ZMAT4,non_coding_transcript_exon_variant,,ENST00000518242,,n.289C>T,MODIFIER,,,,-1" "A" "ENSG00000165061" "ENST00000297737" "Transcript" "synonymous_variant" "synonymous_variant" "444/2466" "297/690" "99/229" "H" "caC/caT" "rs189553545" 1 NA -1 "ZMAT4" "HGNC" "HGNC:25844" "protein_coding" "YES" "CCDS34885.1" "ENSP00000297737" "Q9H898" NA NA "NM_024645.2" NA NA "4/7" NA "SMART_domains:SM00451;SMART_domains:SM00355;Superfamily_domains:SSF57667" 4e-04 8e-04 0 NA 0 0.001 0 NA NA NA NA NA NA NA NA NA "LOW" 1 "SNV" 2 NA NA 1 5.765e-05 5.79e-05 0.0002885 8.649e-05 0 0 3.005e-05 0 6.171e-05 NA "PASS" "TTGGCGTGGAT" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "gdc_pon;wga_pair" "COSM4742863" TRUE "Unknown"
"37" "RGS22" 26166 "BI" "GRCh38" "chr8" 100071425 100071425 "+" "Missense_Mutation" "SNP" "C" "C" "G" "novel" NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.538G>C" "p.Ala180Pro" "p.A180P" "ENST00000360863" "6/28" 79 48 31 246 NA NA "RGS22,missense_variant,p.A180P,ENST00000360863,NM_015668.4,c.538G>C,MODERATE,YES,tolerated(0.33),benign(0.002),-1;RGS22,missense_variant,p.A180P,ENST00000617334,,c.538G>C,MODERATE,,tolerated(0.28),benign(0.001),-1;RGS22,missense_variant,p.A180P,ENST00000523437,NM_001286692.1,c.538G>C,MODERATE,,tolerated(0.28),benign(0.001),-1;RGS22,missense_variant,p.A84P,ENST00000519092,,c.250G>C,MODERATE,,tolerated(0.29),benign(0.002),-1;RGS22,missense_variant,p.A99P,ENST00000520117,,c.295G>C,MODERATE,,tolerated(0.28),benign(0.005),-1;RGS22,intron_variant,,ENST00000523287,NM_001286693.1,c.52-5129G>C,MODIFIER,,,,-1;RGS22,intron_variant,,ENST00000517828,,c.111+22022G>C,MODIFIER,,,,-1;RGS22,downstream_gene_variant,,ENST00000519408,,,MODIFIER,,,,-1;RGS22,missense_variant,p.A180P,ENST00000519725,,c.538G>C,MODERATE,,tolerated(0.28),benign(0.002),-1;RGS22,non_coding_transcript_exon_variant,,ENST00000520923,,n.340G>C,MODIFIER,,,,-1" "G" "ENSG00000132554" "ENST00000360863" "Transcript" "missense_variant" "missense_variant" "733/4296" "538/3795" "180/1264" "A/P" "Gcc/Ccc" NA 1 NA -1 "RGS22" "HGNC" "HGNC:24499" "protein_coding" "YES" "CCDS43758.1" "ENSP00000354109" "Q8NE09" NA "UPI0000E5AF25" "NM_015668.4" "tolerated(0.33)" "benign(0.002)" "6/28" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "MODERATE" 1 "SNV" 1 NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "AGTGGCAGGAG" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" NA TRUE "Unknown"
"38" "ZHX1" 11244 "BI" "GRCh38" "chr8" 123255938 123255938 "+" "Silent" "SNP" "G" "G" "A" "novel" NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.9C>T" "p.=" "p.S3S" "ENST00000297857" "3/4" 378 328 48 294 NA NA "ZHX1,synonymous_variant,p.S3S,ENST00000297857,NM_001017926.2,c.9C>T,LOW,YES,,,-1;ZHX1,synonymous_variant,p.S3S,ENST00000395571,NM_007222.4,c.9C>T,LOW,,,,-1;ZHX1,synonymous_variant,p.S3S,ENST00000522655,,c.9C>T,LOW,,,,-1;ZHX1-C8orf76,intron_variant,,ENST00000622816,NM_001204180.1,c.21+11335C>T,MODIFIER,YES,,,-1;ZHX1-C8orf76,intron_variant,,ENST00000357082,,c.21+11335C>T,MODIFIER,,,,-1;ZHX1,upstream_gene_variant,,ENST00000602651,,,MODIFIER,,,,-1;ZHX1,non_coding_transcript_exon_variant,,ENST00000522595,,n.711C>T,MODIFIER,,,,-1;ZHX1,non_coding_transcript_exon_variant,,ENST00000524267,,n.596C>T,MODIFIER,,,,-1;ZHX1,intron_variant,,ENST00000517516,,n.120-5618C>T,MODIFIER,,,,-1;ZHX1,downstream_gene_variant,,ENST00000480132,,,MODIFIER,,,,-1" "A" "ENSG00000165156" "ENST00000297857" "Transcript" "synonymous_variant" "synonymous_variant" "714/5200" "9/2622" "3/873" "S" "agC/agT" NA 1 NA -1 "ZHX1" "HGNC" "HGNC:12871" "protein_coding" "YES" "CCDS6342.1" "ENSP00000297857" "Q9UKY1" "A0A024R9F1" "UPI000007404F" "NM_001017926.2" NA NA "3/4" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "LOW" 1 "SNV" 5 NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "CGCCTGCTTGC" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" NA TRUE "Unknown"
"39" "FRMPD1" 22844 "BI" "GRCh38" "chr9" 37737220 37737220 "+" "Missense_Mutation" "SNP" "C" "C" "T" "rs571037699" "by1000G;byFrequency" "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.1526C>T" "p.Ala509Val" "p.A509V" "ENST00000377765" "14/16" 159 91 68 194 NA NA "FRMPD1,missense_variant,p.A509V,ENST00000539465,,c.1526C>T,MODERATE,YES,tolerated(1),benign(0),1;FRMPD1,missense_variant,p.A509V,ENST00000377765,NM_014907.2,c.1526C>T,MODERATE,,tolerated(1),benign(0),1;RP11-613M10.9,intron_variant,,ENST00000540557,,c.*911-9192G>A,MODIFIER,YES,,,-1" "T" "ENSG00000070601" "ENST00000377765" "Transcript" "missense_variant" "missense_variant" "1625/4971" "1526/4737" "509/1578" "A/V" "gCg/gTg" "rs571037699" 1 NA 1 "FRMPD1" "HGNC" "HGNC:29159" "protein_coding" NA "CCDS6612.1" "ENSP00000366995" "Q5SYB0" NA NA "NM_014907.2" "tolerated(1)" "benign(0)" "14/16" NA NA 8e-04 0 0 NA 0 0 0.0041 NA NA NA NA NA NA NA NA NA "MODERATE" NA "SNV" 1 NA NA 1 0.0003706 0.0003708 9.614e-05 8.64e-05 0.0001156 0 4.497e-05 0 0.002363 NA "PASS" "ACAAGCGCACC" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "common_in_exac;wga_pair" "COSM4382081;COSM4382082" TRUE "Unknown"
"40" "PTCH1" 5727 "BI" "GRCh38" "chr9" 95447352 95447352 "+" "Missense_Mutation" "SNP" "G" "G" "A" "rs747093389" "byFrequency" "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.3904C>T" "p.Pro1302Ser" "p.P1302S" "ENST00000331920" "23/24" 37 21 16 22 NA NA "PTCH1,missense_variant,p.P1236S,ENST00000430669,,c.3706C>T,MODERATE,,tolerated_low_confidence(0.34),benign(0),-1;PTCH1,missense_variant,p.P1302S,ENST00000331920,NM_000264.3,c.3904C>T,MODERATE,YES,tolerated_low_confidence(0.3),benign(0.001),-1;PTCH1,missense_variant,p.P1236S,ENST00000437951,NM_001083602.1,c.3706C>T,MODERATE,,tolerated_low_confidence(0.34),benign(0),-1;PTCH1,missense_variant,p.P1151S,ENST00000418258,NM_001083607.1,c.3451C>T,MODERATE,,tolerated_low_confidence(0.32),benign(0.001),-1;PTCH1,missense_variant,p.P1151S,ENST00000421141,NM_001083605.1&NM_001083604.1,c.3451C>T,MODERATE,,tolerated_low_confidence(0.32),benign(0.001),-1;PTCH1,missense_variant,p.P1151S,ENST00000429896,NM_001083606.1,c.3451C>T,MODERATE,,tolerated_low_confidence(0.32),benign(0.001),-1;PTCH1,missense_variant,p.P1301S,ENST00000375274,NM_001083603.1,c.3901C>T,MODERATE,,tolerated_low_confidence(0.22),benign(0.001),-1;PTCH1,3_prime_UTR_variant,,ENST00000375290,,c.*5749C>T,MODIFIER,,,,-1;PTCH1,non_coding_transcript_exon_variant,,ENST00000546744,,n.968C>T,MODIFIER,,,,-1" "A" "ENSG00000185920" "ENST00000331920" "Transcript" "missense_variant" "missense_variant" "4204/8057" "3904/4344" "1302/1447" "P/S" "Ccc/Tcc" "rs747093389" 1 NA -1 "PTCH1" "HGNC" "HGNC:9585" "protein_coding" "YES" "CCDS6714.1" "ENSP00000332353" "Q13635" NA "UPI00001AFF9C" "NM_000264.3" "tolerated_low_confidence(0.3)" "benign(0.001)" "23/24" NA "Low_complexity_(Seg):Seg" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "MODERATE" 1 "SNV" 5 NA NA 1 1.65e-05 1.716e-05 0 0 0 0.000303 0 0 0 NA "PASS" "GCGGGGCTGCT" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" NA TRUE "Unknown"
"41" "WAPAL" 23063 "BI" "GRCh38" "chr10" 86500498 86500498 "+" "Nonsense_Mutation" "SNP" "C" "C" "A" "novel" NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.745G>T" "p.Glu249Ter" "p.E249*" "ENST00000298767" "3/19" 138 110 28 310 NA NA "WAPAL,stop_gained,p.E249*,ENST00000298767,NM_015045.2,c.745G>T,HIGH,YES,,,-1;WAPAL,stop_gained,p.E249*,ENST00000618527,,c.745G>T,HIGH,,,,-1;WAPAL,5_prime_UTR_variant,,ENST00000263070,,c.-1455G>T,MODIFIER,,,,-1" "A" "ENSG00000062650" "ENST00000298767" "Transcript" "stop_gained" "stop_gained" "1218/6333" "745/3573" "249/1190" "E/*" "Gaa/Taa" NA 1 NA -1 "WAPAL" "HGNC" "HGNC:23293" "protein_coding" "YES" "CCDS7375.1" "ENSP00000298767" "Q7Z5K2" NA "UPI00001AE41A" "NM_015045.2" NA NA "3/19" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "HIGH" 1 "SNV" 1 NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "GTCTTCTGATC" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" NA TRUE "Unknown"
"42" "PTEN" 5728 "BI" "GRCh38" "chr10" 87961119 87961119 "+" "Splice_Site" "SNP" "G" "G" "C" "rs786201041" "byCluster" "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.1026+1G>C" NA "p.X342_splice" "ENST00000371953" NA 52 29 23 269 NA NA "PTEN,splice_donor_variant,p.X342_splice,ENST00000371953,NM_000314.4,c.1026+1G>C,HIGH,YES,,,1;PTEN,missense_variant,p.V152L,ENST00000472832,,c.454G>C,MODERATE,,deleterious(0),probably_damaging(0.998),1" "C" "ENSG00000171862" "ENST00000371953" "Transcript" "splice_donor_variant" "splice_donor_variant" "-/9027" "1026/1212" "342/403" NA NA "rs786201041" 1 NA 1 "PTEN" "HGNC" "HGNC:9588" "protein_coding" "YES" "CCDS31238.1" "ENSP00000361021" "P60484" "F6KD01" "UPI00001328C5" "NM_000314.4" NA NA NA "8/8" NA NA NA NA NA NA NA NA NA NA "likely_pathogenic;pathogenic" NA NA NA NA NA NA "HIGH" 1 "SNV" 1 NA "1" 1 NA NA NA NA NA NA NA NA NA NA "PASS" "TTAAGGTCAGT" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" "COSM3441286" TRUE "Unknown"
"43" "AMPD3" 272 "BI" "GRCh38" "chr11" 10478726 10478726 "+" "Missense_Mutation" "SNP" "C" "C" "T" "novel" NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.422C>T" "p.Ala141Val" "p.A141V" "ENST00000396553" "3/15" 35 20 15 28 NA NA "AMPD3,missense_variant,p.A150V,ENST00000396554,NM_000480.2,c.449C>T,MODERATE,YES,tolerated(0.08),benign(0.181),1;AMPD3,missense_variant,p.A141V,ENST00000396553,NM_001025389.1,c.422C>T,MODERATE,,tolerated(0.08),benign(0.181),1;AMPD3,missense_variant,p.A141V,ENST00000529507,NM_001172430.1,c.422C>T,MODERATE,,tolerated(0.08),benign(0.181),1;AMPD3,missense_variant,p.A148V,ENST00000528723,NM_001025390.1,c.443C>T,MODERATE,,tolerated(0.08),benign(0.181),1;AMPD3,missense_variant,p.A141V,ENST00000524866,,c.422C>T,MODERATE,,tolerated(0.05),benign(0.181),1;AMPD3,intron_variant,,ENST00000444303,NM_001172431.1,c.-51-3337C>T,MODIFIER,,,,1;AMPD3,downstream_gene_variant,,ENST00000532250,,,MODIFIER,,,,1;AMPD3,intron_variant,,ENST00000529835,,n.422-3337C>T,MODIFIER,,,,1;AMPD3,missense_variant,p.A150V,ENST00000534047,,c.449C>T,MODERATE,,tolerated(0.05),probably_damaging(0.994),1;AMPD3,missense_variant,p.A141V,ENST00000529834,,c.422C>T,MODERATE,,tolerated(0.06),benign(0.181),1;AMPD3,upstream_gene_variant,,ENST00000531227,,,MODIFIER,,,,1" "T" "ENSG00000133805" "ENST00000396553" "Transcript" "missense_variant" "missense_variant" "556/3680" "422/2304" "141/767" "A/V" "gCc/gTc" NA 1 NA 1 "AMPD3" "HGNC" "HGNC:470" "protein_coding" NA "CCDS41617.1" "ENSP00000379801" "Q01432" NA "UPI0000125959" "NM_001025389.1" "tolerated(0.08)" "benign(0.181)" "3/15" NA "Superfamily_domains:SSF51556;PIRSF_domain:PIRSF001251" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "MODERATE" NA "SNV" 1 NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "CTGTGCCGGGG" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" NA TRUE "Unknown"
"44" "OR8K1" 390157 "BI" "GRCh38" "chr11" 56346113 56346113 "+" "Missense_Mutation" "SNP" "C" "C" "A" "rs769004561" NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.75C>A" "p.Asp25Glu" "p.D25E" "ENST00000279783" "1/1" 127 102 25 225 NA NA "OR8K1,missense_variant,p.D25E,ENST00000279783,NM_001002907.1,c.75C>A,MODERATE,YES,tolerated_low_confidence(0.07),benign(0.038),1" "A" "ENSG00000150261" "ENST00000279783" "Transcript" "missense_variant" "missense_variant" "75/960" "75/960" "25/319" "D/E" "gaC/gaA" "rs769004561" 1 NA 1 "OR8K1" "HGNC" "HGNC:14831" "protein_coding" "YES" "CCDS31528.1" "ENSP00000279783" "Q8NGG5" NA "UPI0000041BC6" "NM_001002907.1" "tolerated_low_confidence(0.07)" "benign(0.038)" "1/1" NA "Superfamily_domains:SSF81321" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "MODERATE" 1 "SNV" NA NA NA 1 8.237e-06 8.247e-06 0 0 0 0 1.5e-05 0 0 NA "PASS" "ACAGACAACCC" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" "COSM3967610" TRUE "Unknown"
"45" "OR5AR1" 219493 "BI" "GRCh38" "chr11" 56664168 56664168 "+" "Silent" "SNP" "C" "C" "A" "novel" NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.483C>A" "p.=" "p.T161T" "ENST00000302969" "1/1" 488 310 175 588 NA NA "OR5AR1,synonymous_variant,p.T161T,ENST00000302969,,c.483C>A,LOW,YES,,,1;OR5AR1,synonymous_variant,p.T161T,ENST00000625024,NM_001004730.1,c.483C>A,LOW,YES,,,1;OR5AR1,synonymous_variant,p.T161T,ENST00000624596,,c.483C>A,LOW,,,,1;OR2AH1P,downstream_gene_variant,,ENST00000425717,,,MODIFIER,YES,,,-1" "A" "ENSG00000172459" "ENST00000302969" "Transcript" "synonymous_variant" "synonymous_variant" "507/1026" "483/933" "161/310" "T" "acC/acA" NA 1 NA 1 "OR5AR1" "HGNC" "HGNC:15260" "protein_coding" "YES" "CCDS31535.1" "ENSP00000302639" "Q8NGP9" NA "UPI0000041C93" NA NA NA "1/1" NA "Pfam_domain:PF00001;Transmembrane_helices:Tmhmm;PROSITE_profiles:PS50262;Superfamily_domains:SSF81321" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "LOW" 1 "SNV" NA NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "ACTACCCTCAC" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" NA TRUE "Unknown"
"46" "SF3B2" 10992 "BI" "GRCh38" "chr11" 66068867 66068867 "+" "3'UTR" "SNP" "G" "G" "A" "novel" NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.*122G>A" NA NA "ENST00000322535" "22/22" 11 6 5 24 NA NA "SF3B2,3_prime_UTR_variant,,ENST00000528302,,c.*122G>A,MODIFIER,,,,1;SF3B2,3_prime_UTR_variant,,ENST00000322535,NM_006842.2,c.*122G>A,MODIFIER,YES,,,1;SF3B2,3_prime_UTR_variant,,ENST00000610523,,c.*122G>A,MODIFIER,,,,1;SF3B2,3_prime_UTR_variant,,ENST00000530981,,c.*122G>A,MODIFIER,,,,1;PACS1,upstream_gene_variant,,ENST00000320580,NM_018026.3,,MODIFIER,YES,,,1;RP11-1167A19.2,intron_variant,,ENST00000529036,,n.239+514C>T,MODIFIER,YES,,,-1;SF3B2,downstream_gene_variant,,ENST00000534765,,,MODIFIER,,,,1;PACS1,upstream_gene_variant,,ENST00000527224,,,MODIFIER,,,,1" "A" "ENSG00000087365" "ENST00000322535" "Transcript" "3_prime_UTR_variant" "3_prime_UTR_variant" "2859/2903" "-/2688" "-/895" NA NA NA 1 NA 1 "SF3B2" "HGNC" "HGNC:10769" "protein_coding" "YES" "CCDS31612.1" "ENSP00000318861" "Q13435" NA "UPI00001C1F20" "NM_006842.2" NA NA "22/22" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "MODIFIER" 1 "SNV" 1 NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "GTTTTGTAAAT" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" NA FALSE "Unknown"
"47" "SLC2A3" 6515 "BI" "GRCh38" "chr12" 7931437 7931437 "+" "Nonsense_Mutation" "SNP" "G" "G" "T" NA NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.318C>A" "p.Cys106Ter" "p.C106*" "ENST00000075120" "4/10" 154 132 20 209 NA NA "SLC2A3,stop_gained,p.C106*,ENST00000075120,NM_006931.2,c.318C>A,HIGH,YES,,,-1;SLC2A3,stop_gained,p.C75*,ENST00000544291,,c.225C>A,HIGH,,,,-1;SLC2A3,3_prime_UTR_variant,,ENST00000544936,,c.*203C>A,MODIFIER,,,,-1;SLC2A3,non_coding_transcript_exon_variant,,ENST00000486749,,n.451C>A,MODIFIER,,,,-1;SLC2A3,non_coding_transcript_exon_variant,,ENST00000495813,,n.453C>A,MODIFIER,,,,-1;SLC2A3,upstream_gene_variant,,ENST00000490763,,,MODIFIER,,,,-1;SLC2A3,upstream_gene_variant,,ENST00000479059,,,MODIFIER,,,,-1;SLC2A3,downstream_gene_variant,,ENST00000476634,,,MODIFIER,,,,-1;SLC2A3,downstream_gene_variant,,ENST00000541671,,,MODIFIER,,,,-1" "T" "ENSG00000059804" "ENST00000075120" "Transcript" "stop_gained" "stop_gained" "559/3915" "318/1491" "106/496" "C/*" "tgC/tgA" NA 1 NA -1 "SLC2A3" "HGNC" "HGNC:11007" "protein_coding" "YES" "CCDS8586.1" "ENSP00000075120" "P11169" NA "UPI0000001C7D" "NM_006931.2" NA NA "4/10" NA "Pfam_domain:PF00083;Pfam_domain:PF07690;Transmembrane_helices:Tmhmm;TIGRFAM_domain:TIGR00879;PROSITE_profiles:PS50850;Superfamily_domains:SSF103473" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "HIGH" 1 "SNV" 1 NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "ATAAAGCAGCC" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" "COSM943807" TRUE "Unknown"
"48" "STYK1" 55359 "BI" "GRCh38" "chr12" 10634093 10634093 "+" "Silent" "SNP" "G" "G" "A" "novel" NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.84C>T" "p.=" "p.I28I" "ENST00000075503" "4/11" 184 143 41 244 NA NA "STYK1,synonymous_variant,p.I28I,ENST00000075503,NM_018423.2,c.84C>T,LOW,YES,,,-1;STYK1,synonymous_variant,p.I28I,ENST00000538867,,c.84C>T,LOW,,,,-1;STYK1,synonymous_variant,p.I28I,ENST00000542562,,c.84C>T,LOW,,,,-1;STYK1,synonymous_variant,p.I28I,ENST00000541561,,c.84C>T,LOW,,,,-1;STYK1,synonymous_variant,p.I28I,ENST00000535345,,c.84C>T,LOW,,,,-1;STYK1,upstream_gene_variant,,ENST00000542924,,,MODIFIER,,,,-1" "A" "ENSG00000060140" "ENST00000075503" "Transcript" "synonymous_variant" "synonymous_variant" "605/2995" "84/1269" "28/422" "I" "atC/atT" NA 1 NA -1 "STYK1" "HGNC" "HGNC:18889" "protein_coding" "YES" "CCDS8629.1" "ENSP00000075503" "Q6J9G0" NA "UPI000013C57C" "NM_018423.2" NA NA "4/11" NA "Transmembrane_helices:Tmhmm" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "LOW" 1 "SNV" 1 NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "GGGACGATAAT" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" NA TRUE "Unknown"
"49" "ALG10B" 144245 "BI" "GRCh38" "chr12" 38320751 38320751 "+" "Nonsense_Mutation" "SNP" "G" "G" "A" "novel" NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.960G>A" "p.Trp320Ter" "p.W320*" "ENST00000308742" "3/3" 121 88 33 208 NA NA "ALG10B,stop_gained,p.W320*,ENST00000308742,NM_001013620.3,c.960G>A,HIGH,YES,,,1;ALG10B,intron_variant,,ENST00000551464,,c.369+2293G>A,MODIFIER,,,,1;AC117372.1,downstream_gene_variant,,ENST00000401168,,,MODIFIER,YES,,,-1;ALG10B,3_prime_UTR_variant,,ENST00000548240,,c.*700G>A,MODIFIER,,,,1;ALG10B,downstream_gene_variant,,ENST00000553138,,,MODIFIER,,,,1" "A" "ENSG00000175548" "ENST00000308742" "Transcript" "stop_gained" "stop_gained" "1276/10253" "960/1422" "320/473" "W/*" "tgG/tgA" NA 1 NA 1 "ALG10B" "HGNC" "HGNC:31088" "protein_coding" "YES" "CCDS31772.1" "ENSP00000310120" "Q5I7T1" NA "UPI000013EDA4" "NM_001013620.3" NA NA "3/3" NA "Transmembrane_helices:Tmhmm;Pfam_domain:PF04922;PIRSF_domain:PIRSF028810" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "HIGH" 1 "SNV" 1 NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "GTTTGGAAACA" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" NA TRUE "Unknown"
"50" "ALG10B" 144245 "BI" "GRCh38" "chr12" 38320759 38320759 "+" "Missense_Mutation" "SNP" "G" "G" "A" "novel" NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.968G>A" "p.Gly323Glu" "p.G323E" "ENST00000308742" "3/3" 112 80 32 211 NA NA "ALG10B,missense_variant,p.G323E,ENST00000308742,NM_001013620.3,c.968G>A,MODERATE,YES,tolerated(0.36),benign(0.001),1;ALG10B,intron_variant,,ENST00000551464,,c.369+2301G>A,MODIFIER,,,,1;AC117372.1,downstream_gene_variant,,ENST00000401168,,,MODIFIER,YES,,,-1;ALG10B,3_prime_UTR_variant,,ENST00000548240,,c.*708G>A,MODIFIER,,,,1;ALG10B,downstream_gene_variant,,ENST00000553138,,,MODIFIER,,,,1" "A" "ENSG00000175548" "ENST00000308742" "Transcript" "missense_variant" "missense_variant" "1284/10253" "968/1422" "323/473" "G/E" "gGa/gAa" NA 1 NA 1 "ALG10B" "HGNC" "HGNC:31088" "protein_coding" "YES" "CCDS31772.1" "ENSP00000310120" "Q5I7T1" NA "UPI000013EDA4" "NM_001013620.3" "tolerated(0.36)" "benign(0.001)" "3/3" NA "Transmembrane_helices:Tmhmm;Pfam_domain:PF04922;PIRSF_domain:PIRSF028810" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "MODERATE" 1 "SNV" 1 NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "ACATGGAATTC" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" NA TRUE "Unknown"
"51" "ALG10B" 144245 "BI" "GRCh38" "chr12" 38321287 38321287 "+" "3'UTR" "SNP" "G" "G" "T" "novel" NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.*74G>T" NA NA "ENST00000308742" "3/3" 23 16 7 55 NA NA "ALG10B,3_prime_UTR_variant,,ENST00000308742,NM_001013620.3,c.*74G>T,MODIFIER,YES,,,1;ALG10B,intron_variant,,ENST00000551464,,c.370-2626G>T,MODIFIER,,,,1;AC117372.1,downstream_gene_variant,,ENST00000401168,,,MODIFIER,YES,,,-1;ALG10B,3_prime_UTR_variant,,ENST00000548240,,c.*1236G>T,MODIFIER,,,,1;ALG10B,downstream_gene_variant,,ENST00000553138,,,MODIFIER,,,,1" "T" "ENSG00000175548" "ENST00000308742" "Transcript" "3_prime_UTR_variant" "3_prime_UTR_variant" "1812/10253" "-/1422" "-/473" NA NA NA 1 NA 1 "ALG10B" "HGNC" "HGNC:31088" "protein_coding" "YES" "CCDS31772.1" "ENSP00000310120" "Q5I7T1" NA "UPI000013EDA4" "NM_001013620.3" NA NA "3/3" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "MODIFIER" 1 "SNV" 1 NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "TAGGTGGAAAA" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" NA TRUE "Unknown"
"52" "NCKAP1L" 3071 "BI" "GRCh38" "chr12" 54520756 54520756 "+" "Missense_Mutation" "SNP" "G" "G" "A" "rs752125351" "byFrequency" "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.1688G>A" "p.Arg563His" "p.R563H" "ENST00000293373" "17/31" 661 252 407 1138 NA NA "NCKAP1L,missense_variant,p.R563H,ENST00000293373,NM_005337.4,c.1688G>A,MODERATE,YES,deleterious(0),probably_damaging(0.995),1;NCKAP1L,missense_variant,p.R513H,ENST00000545638,NM_001184976.1,c.1538G>A,MODERATE,,deleterious(0),probably_damaging(0.995),1;NCKAP1L,downstream_gene_variant,,ENST00000552211,,,MODIFIER,,,,1;NCKAP1L,3_prime_UTR_variant,,ENST00000548221,,c.*393G>A,MODIFIER,,,,1;NCKAP1L,non_coding_transcript_exon_variant,,ENST00000549451,,n.559G>A,MODIFIER,,,,1" "A" "ENSG00000123338" "ENST00000293373" "Transcript" "missense_variant" "missense_variant" "1767/9016" "1688/3384" "563/1127" "R/H" "cGt/cAt" "rs752125351" 1 NA 1 "NCKAP1L" "HGNC" "HGNC:4862" "protein_coding" "YES" "CCDS31813.1" "ENSP00000293373" "P55160" NA "UPI00001C0439" "NM_005337.4" "deleterious(0)" "probably_damaging(0.995)" "17/31" NA "Pfam_domain:PF09735" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "MODERATE" 1 "SNV" 1 NA NA 1 7.413e-05 7.413e-05 0 8.637e-05 0 0 0 0 0.0004845 NA "PASS" "GTTGCGTTATG" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "common_in_exac;wga_pair" "COSM3398862" TRUE "Unknown"
"53" "RDH16" 8608 "BI" "GRCh38" "chr12" 56957546 56957546 "+" "5'UTR" "SNP" "G" "G" "C" "novel" NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.-84C>G" NA NA "ENST00000398138" "1/4" 41 27 14 40 NA NA "RDH16,5_prime_UTR_variant,,ENST00000398138,NM_003708.3,c.-84C>G,MODIFIER,YES,,,-1;RDH16,non_coding_transcript_exon_variant,,ENST00000360752,,n.1829C>G,MODIFIER,,,,-1" "C" "ENSG00000139547" "ENST00000398138" "Transcript" "5_prime_UTR_variant" "5_prime_UTR_variant" "774/2409" "-/954" "-/317" NA NA NA 1 NA -1 "RDH16" "HGNC" "HGNC:29674" "protein_coding" "YES" "CCDS41797.1" "ENSP00000381206" "O75452" NA "UPI000013D71C" "NM_003708.3" NA NA "1/4" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "MODIFIER" 1 "SNV" 1 NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "ACACAGAGGGC" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" NA TRUE "Unknown"
"54" "PIP4K2C" 79837 "BI" "GRCh38" "chr12" 57594086 57594086 "+" "Missense_Mutation" "SNP" "G" "G" "A" "rs774720885" NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.236G>A" "p.Ser79Asn" "p.S79N" "ENST00000354947" "2/10" 144 93 51 103 NA NA "PIP4K2C,missense_variant,p.S79N,ENST00000354947,,c.236G>A,MODERATE,YES,tolerated(0.38),benign(0.011),1;PIP4K2C,missense_variant,p.S79N,ENST00000540759,NM_024779.4&NM_001146258.1,c.236G>A,MODERATE,,tolerated(0.38),benign(0.011),1;PIP4K2C,missense_variant,p.S79N,ENST00000422156,NM_001146260.1,c.236G>A,MODERATE,,tolerated(0.39),benign(0.002),1;PIP4K2C,missense_variant,p.S79N,ENST00000550465,NM_001146259.1,c.236G>A,MODERATE,,tolerated(0.39),benign(0.004),1;PIP4K2C,missense_variant,p.S58N,ENST00000551772,,c.173G>A,MODERATE,,tolerated(0.37),benign(0.004),1;PIP4K2C,missense_variant,p.S79N,ENST00000550095,,c.236G>A,MODERATE,,tolerated(0.33),benign(0.011),1;PIP4K2C,3_prime_UTR_variant,,ENST00000550360,,c.*54G>A,MODIFIER,,,,1" "A" "ENSG00000166908" "ENST00000354947" "Transcript" "missense_variant" "missense_variant" "252/2924" "236/1266" "79/421" "S/N" "aGc/aAc" "rs774720885" 1 NA 1 "PIP4K2C" "HGNC" "HGNC:23786" "protein_coding" "YES" "CCDS8946.1" "ENSP00000347032" "Q8TBX8" NA "UPI000003F553" NA "tolerated(0.38)" "benign(0.011)" "2/10" NA "SMART_domains:SM00330;Superfamily_domains:SSF56104" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "MODERATE" 1 "SNV" 1 NA NA 1 8.236e-06 8.293e-06 0 0 0 0 1.505e-05 0 0 NA "PASS" "GGCCAGCTCCA" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" "COSM942131" TRUE "Unknown"
"55" "ACAD10" 80724 "BI" "GRCh38" "chr12" 111729820 111729820 "+" "Missense_Mutation" "SNP" "C" "C" "T" "rs575221081" "by1000G;byCluster" "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.1258C>T" "p.Arg420Cys" "p.R420C" "ENST00000313698" "10/21" 138 98 40 118 NA NA "ACAD10,missense_variant,p.R451C,ENST00000455480,NM_001136538.1,c.1351C>T,MODERATE,YES,deleterious(0.01),possibly_damaging(0.534),1;ACAD10,missense_variant,p.R420C,ENST00000313698,NM_025247.5,c.1258C>T,MODERATE,,deleterious(0.01),benign(0.095),1;ACAD10,missense_variant,p.R420C,ENST00000549590,,c.1258C>T,MODERATE,,deleterious(0.01),benign(0.297),1;ACAD10,intron_variant,,ENST00000507683,,c.527+1677C>T,MODIFIER,,,,1;ACAD10,intron_variant,,ENST00000515283,,c.-107-14823C>T,MODIFIER,,,,1;ACAD10,intron_variant,,ENST00000552706,,c.553+1677C>T,MODIFIER,,,,1;ACAD10,non_coding_transcript_exon_variant,,ENST00000413681,,n.1443C>T,MODIFIER,,,,1;ACAD10,non_coding_transcript_exon_variant,,ENST00000508303,,n.408C>T,MODIFIER,,,,1;ACAD10,non_coding_transcript_exon_variant,,ENST00000502746,,n.442C>T,MODIFIER,,,,1;ACAD10,downstream_gene_variant,,ENST00000503490,,,MODIFIER,,,,1;ACAD10,upstream_gene_variant,,ENST00000552177,,,MODIFIER,,,,1" "T" "ENSG00000111271" "ENST00000313698" "Transcript" "missense_variant" "missense_variant" "1413/3959" "1258/3180" "420/1059" "R/C" "Cgc/Tgc" "rs575221081" 1 NA 1 "ACAD10" "HGNC" "HGNC:21597" "protein_coding" NA "CCDS31903.1" "ENSP00000325137" "Q6JQN1" NA "UPI000013C8E1" "NM_025247.5" "deleterious(0.01)" "benign(0.095)" "10/21" NA "Pfam_domain:PF01636;Superfamily_domains:SSF56112" 2e-04 0 0 NA 0 0 0.001 NA NA NA NA NA NA NA NA NA "MODERATE" NA "SNV" 1 NA NA 1 7.413e-05 7.436e-05 0 8.645e-05 0.0001156 0 0 0 0.0004278 NA "PASS" "TTCCACGCCAG" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "common_in_exac;wga_pair" "COSM4038750;COSM4038751" TRUE "Unknown"
"56" "NCOR2" 9612 "BI" "GRCh38" "chr12" 124333182 124333182 "+" "Missense_Mutation" "SNP" "G" "G" "A" "rs753999562" "byFrequency" "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.6703C>T" "p.Arg2235Trp" "p.R2235W" "ENST00000405201" "42/47" 33 11 21 23 NA NA "NCOR2,missense_variant,p.R2235W,ENST00000405201,NM_006312.5,c.6703C>T,MODERATE,YES,,probably_damaging(0.999),-1;NCOR2,missense_variant,p.R2225W,ENST00000404621,NM_001077261.3,c.6673C>T,MODERATE,,,probably_damaging(0.982),-1;NCOR2,missense_variant,p.R2225W,ENST00000429285,NM_001206654.1,c.6673C>T,MODERATE,,,probably_damaging(0.998),-1;NCOR2,missense_variant,p.R1800W,ENST00000356219,,c.5398C>T,MODERATE,,,probably_damaging(0.999),-1;NCOR2,missense_variant,p.R1783W,ENST00000404121,,c.5347C>T,MODERATE,,,probably_damaging(0.998),-1;NCOR2,missense_variant,p.R26W,ENST00000440337,,c.75C>T,MODERATE,,deleterious(0),probably_damaging(0.994),-1;NCOR2,upstream_gene_variant,,ENST00000418829,,,MODIFIER,,,,-1;NCOR2,downstream_gene_variant,,ENST00000440187,,,MODIFIER,,,,-1;MIR6880,downstream_gene_variant,,ENST00000622851,,,MODIFIER,YES,,,-1;NCOR2,non_coding_transcript_exon_variant,,ENST00000461081,,n.1865C>T,MODIFIER,,,,-1;NCOR2,non_coding_transcript_exon_variant,,ENST00000443451,,n.321C>T,MODIFIER,,,,-1;NCOR2,downstream_gene_variant,,ENST00000474079,,,MODIFIER,,,,-1" "A" "ENSG00000196498" "ENST00000405201" "Transcript" "missense_variant" "missense_variant" "6704/8533" "6703/7545" "2235/2514" "R/W" "Cgg/Tgg" "rs753999562" 1 NA -1 "NCOR2" "HGNC" "HGNC:7673" "protein_coding" "YES" "CCDS41858.2" "ENSP00000384018" NA "C9JFD3" "UPI000013D737" "NM_006312.5" NA "probably_damaging(0.999)" "42/47" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "MODERATE" 1 "SNV" 1 NA NA 1 6.613e-05 6.754e-05 0.0001039 0 0 0 0.0001072 0 0 NA "PASS" "ACTCCGGGAGT" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "gdc_pon;wga_pair" NA TRUE "Unknown"
"57" "TMEM132D" 121256 "BI" "GRCh38" "chr12" 129700069 129700069 "+" "Missense_Mutation" "SNP" "C" "C" "A" "novel" NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.709G>T" "p.Gly237Trp" "p.G237W" "ENST00000422113" "2/9" 96 42 54 49 NA NA "TMEM132D,missense_variant,p.G237W,ENST00000422113,NM_133448.2,c.709G>T,MODERATE,YES,deleterious(0.01),benign(0.322),-1;TMEM132D,missense_variant,p.G217W,ENST00000619366,,c.649G>T,MODERATE,,deleterious(0.01),benign(0.137),-1;RP11-174M13.2,upstream_gene_variant,,ENST00000544036,,,MODIFIER,YES,,,-1" "A" "ENSG00000151952" "ENST00000422113" "Transcript" "missense_variant" "missense_variant" "1036/5776" "709/3300" "237/1099" "G/W" "Ggg/Tgg" NA 1 NA -1 "TMEM132D" "HGNC" "HGNC:29411" "protein_coding" "YES" "CCDS9266.1" "ENSP00000408581" "Q14C87" NA "UPI000023759C" "NM_133448.2" "deleterious(0.01)" "benign(0.322)" "2/9" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "MODERATE" 1 "SNV" 1 NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "GTCCCCTCTCT" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" NA TRUE "Unknown"
"58" "TNFSF11" 8600 "BI" "GRCh38" "chr13" 42606826 42606826 "+" "Nonsense_Mutation" "SNP" "G" "G" "T" "novel" NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.862G>T" "p.Glu288Ter" "p.E288*" "ENST00000398795" "5/5" 341 288 53 257 NA NA "TNFSF11,stop_gained,p.E288*,ENST00000398795,NM_003701.3,c.862G>T,HIGH,YES,,,1;TNFSF11,stop_gained,p.E215*,ENST00000405262,,c.643G>T,HIGH,,,,1;TNFSF11,stop_gained,p.E215*,ENST00000358545,NM_033012.3,c.643G>T,HIGH,,,,1;TNFSF11,stop_gained,p.E241*,ENST00000239849,,c.721G>T,HIGH,,,,1;TNFSF11,stop_gained,p.E215*,ENST00000544862,,c.643G>T,HIGH,,,,1" "T" "ENSG00000120659" "ENST00000398795" "Transcript" "stop_gained" "stop_gained" "1013/2199" "862/954" "288/317" "E/*" "Gaa/Taa" NA 1 NA 1 "TNFSF11" "HGNC" "HGNC:11926" "protein_coding" "YES" "CCDS9384.1" "ENSP00000381775" "O14788" "Q5T9Y4" "UPI000003BC8E" "NM_003701.3" NA NA "5/5" NA "Pfam_domain:PF00229;PROSITE_profiles:PS50049;SMART_domains:SM00207;Superfamily_domains:SSF49842;PIRSF_domain:PIRSF038013" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "HIGH" 1 "SNV" 1 NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "GAGAGGAAATC" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" NA TRUE "Unknown"
"59" "FAM124A" 220108 "BI" "GRCh38" "chr13" 51252157 51252157 "+" "Missense_Mutation" "SNP" "C" "C" "T" NA NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.790C>T" "p.Arg264Cys" "p.R264C" "ENST00000322475" "3/4" 88 62 26 89 NA NA "FAM124A,missense_variant,p.R264C,ENST00000322475,NM_001242312.1,c.790C>T,MODERATE,,deleterious(0),probably_damaging(1),1;FAM124A,missense_variant,p.R264C,ENST00000615498,,c.790C>T,MODERATE,,deleterious(0),probably_damaging(0.999),1;FAM124A,missense_variant,p.R264C,ENST00000614765,,c.790C>T,MODERATE,,deleterious(0),probably_damaging(0.999),1;FAM124A,missense_variant,p.R300C,ENST00000280057,NM_145019.3,c.898C>T,MODERATE,YES,deleterious(0),probably_damaging(1),1" "T" "ENSG00000150510" "ENST00000322475" "Transcript" "missense_variant" "missense_variant" "925/4761" "790/1641" "264/546" "R/C" "Cgc/Tgc" NA 1 NA 1 "FAM124A" "HGNC" "HGNC:26413" "protein_coding" NA "CCDS55900.1" "ENSP00000324625" "Q86V42" NA NA "NM_001242312.1" "deleterious(0)" "probably_damaging(1)" "3/4" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "MODERATE" NA "SNV" 1 NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "AGGGGCGCTGG" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" "COSM1367403" TRUE "Unknown"
"60" "RALGAPA1" 253959 "BI" "GRCh38" "chr14" 35750623 35750623 "+" "Silent" "SNP" "T" "T" "A" "novel" NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.870A>T" "p.=" "p.A290A" "ENST00000389698" "9/41" 114 101 13 249 NA NA "RALGAPA1,synonymous_variant,p.A290A,ENST00000307138,NM_194301.2,c.870A>T,LOW,YES,,,-1;RALGAPA1,synonymous_variant,p.A290A,ENST00000389698,NM_014990.1,c.870A>T,LOW,,,,-1;RALGAPA1,synonymous_variant,p.A290A,ENST00000382366,NM_001283043.1,c.870A>T,LOW,,,,-1;RALGAPA1,synonymous_variant,p.A290A,ENST00000553892,NM_001283044.1,c.870A>T,LOW,,,,-1;RALGAPA1,non_coding_transcript_exon_variant,,ENST00000554704,,n.352A>T,MODIFIER,,,,-1;RALGAPA1,intron_variant,,ENST00000555828,,n.93-1799A>T,MODIFIER,,,,-1;RALGAPA1,non_coding_transcript_exon_variant,,ENST00000554652,,n.389A>T,MODIFIER,,,,-1;RALGAPA1,upstream_gene_variant,,ENST00000557104,,,MODIFIER,,,,-1" "A" "ENSG00000174373" "ENST00000389698" "Transcript" "synonymous_variant" "synonymous_variant" "1261/7864" "870/6111" "290/2036" "A" "gcA/gcT" NA 1 NA -1 "RALGAPA1" "HGNC" "HGNC:17770" "protein_coding" NA "CCDS32065.1" "ENSP00000374348" "Q6GYQ0" NA "UPI00003B5C50" "NM_014990.1" NA NA "9/41" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "LOW" NA "SNV" 1 NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "TAGATTGCTTC" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" NA TRUE "Unknown"
"61" "EHD4" 30844 "BI" "GRCh38" "chr15" 41900686 41900686 "+" "Missense_Mutation" "SNP" "C" "C" "T" "rs554166246" "by1000G;byFrequency" "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.1585G>A" "p.Val529Met" "p.V529M" "ENST00000220325" "6/6" 46 34 11 39 NA NA "EHD4,missense_variant,p.V529M,ENST00000220325,NM_139265.3,c.1585G>A,MODERATE,YES,tolerated(0.06),probably_damaging(0.968),-1;EHD4,missense_variant,p.V528M,ENST00000612090,,c.1582G>A,MODERATE,,tolerated(0.06),probably_damaging(0.989),-1;RP11-23P13.6,downstream_gene_variant,,ENST00000309874,,,MODIFIER,YES,,,1;RP11-23P13.6,downstream_gene_variant,,ENST00000568861,,,MODIFIER,,,,1;RP11-23P13.6,downstream_gene_variant,,ENST00000564432,,,MODIFIER,,,,1;RP11-23P13.6,downstream_gene_variant,,ENST00000562920,,,MODIFIER,,,,1" "T" "ENSG00000103966" "ENST00000220325" "Transcript" "missense_variant" "missense_variant" "1669/6416" "1585/1626" "529/541" "V/M" "Gtg/Atg" "rs554166246" 1 NA -1 "EHD4" "HGNC" "HGNC:3245" "protein_coding" "YES" "CCDS10081.1" "ENSP00000220325" "Q9H223" "A0A024R9N6" "UPI0000129E25" "NM_139265.3" "tolerated(0.06)" "probably_damaging(0.968)" "6/6" NA "Low_complexity_(Seg):Seg;PROSITE_profiles:PS50031;SMART_domains:SM00027;Superfamily_domains:SSF47473" 4e-04 0 0.0029 NA 0 0 0 NA NA NA NA NA NA NA NA NA "MODERATE" 1 "SNV" 1 NA NA 1 1.648e-05 1.808e-05 0 0 0 0 3.284e-05 0 0 NA "PASS" "GGGCACGAGGT" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" NA TRUE "Unknown"
"62" "RP11-20I23.1" 0 "BI" "GRCh38" "chr16" 2519367 2519367 "+" "Missense_Mutation" "SNP" "G" "G" "A" "novel" NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.1115G>A" "p.Arg372His" "p.R372H" "ENST00000564543" "2/3" 169 127 39 285 NA NA "RP11-20I23.1,missense_variant,p.R372H,ENST00000564543,,c.1115G>A,MODERATE,YES,,unknown(0),1;ATP6V0C,missense_variant,p.A77T,ENST00000330398,NM_001694.3,c.229G>A,MODERATE,YES,deleterious(0.05),benign(0.14),1;ATP6V0C,missense_variant,p.A34T,ENST00000564973,,c.100G>A,MODERATE,,deleterious(0.03),benign(0.14),1;ATP6V0C,missense_variant,p.A77T,ENST00000618152,NM_001198569.1,c.229G>A,MODERATE,,deleterious(0.05),benign(0.14),1;ATP6V0C,missense_variant,p.A34T,ENST00000565223,,c.100G>A,MODERATE,,deleterious(0.03),benign(0.14),1;ATP6V0C,missense_variant,p.R59H,ENST00000568562,,c.176G>A,MODERATE,,,unknown(0),1;RP11-20I23.3,intron_variant,,ENST00000569317,,c.80-1617G>A,MODIFIER,YES,,,1;AMDHD2,upstream_gene_variant,,ENST00000302956,NM_015944.3,,MODIFIER,,,,1;AMDHD2,upstream_gene_variant,,ENST00000413459,NM_001145815.1,,MODIFIER,YES,,,1;AMDHD2,upstream_gene_variant,,ENST00000568263,,,MODIFIER,,,,1;AMDHD2,upstream_gene_variant,,ENST00000293971,,,MODIFIER,,,,1;AMDHD2,upstream_gene_variant,,ENST00000566706,,,MODIFIER,,,,1;AMDHD2,upstream_gene_variant,,ENST00000569879,,,MODIFIER,,,,1;AMDHD2,upstream_gene_variant,,ENST00000563556,,,MODIFIER,,,,1;RP11-20I23.2,downstream_gene_variant,,ENST00000624099,,,MODIFIER,YES,,,1;AMDHD2,upstream_gene_variant,,ENST00000563633,,,MODIFIER,,,,1;AMDHD2,upstream_gene_variant,,ENST00000565963,,,MODIFIER,,,,1;AMDHD2,upstream_gene_variant,,ENST00000569219,,,MODIFIER,,,,1;AMDHD2,upstream_gene_variant,,ENST00000567475,,,MODIFIER,,,,1" "A" "ENSG00000260272" "ENST00000564543" "Transcript" "missense_variant" "missense_variant" "1232/1944" "1115/1131" "372/376" "R/H" "cGc/cAc" NA 1 NA 1 "RP11-20I23.1" "Clone_based_vega_gene" NA "protein_coding" "YES" NA "ENSP00000455547" NA "H3BQ06" "UPI0002466D02" NA NA "unknown(0)" "2/3" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "MODERATE" NA "SNV" 2 NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "TCATCGCCAAC" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" NA TRUE "Unknown"
"63" "GRIN2A" 2903 "BI" "GRCh38" "chr16" 9763816 9763816 "+" "Missense_Mutation" "SNP" "C" "C" "T" "novel" NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.3728G>A" "p.Gly1243Glu" "p.G1243E" "ENST00000330684" "13/13" 134 120 13 158 NA NA "GRIN2A,missense_variant,p.G1243E,ENST00000396573,NM_000833.3,c.3728G>A,MODERATE,YES,deleterious(0),probably_damaging(0.994),-1;GRIN2A,missense_variant,p.G1106E,ENST00000396575,,c.3317G>A,MODERATE,,deleterious(0),probably_damaging(0.999),-1;GRIN2A,missense_variant,p.G1243E,ENST00000330684,NM_001134407.1,c.3728G>A,MODERATE,,deleterious(0),probably_damaging(0.994),-1;GRIN2A,missense_variant,p.G1243E,ENST00000562109,NM_001134408.1,c.3728G>A,MODERATE,,deleterious_low_confidence(0),probably_damaging(0.988),-1;GRIN2A,missense_variant,p.G1106E,ENST00000535259,,c.3317G>A,MODERATE,,deleterious_low_confidence(0),probably_damaging(0.964),-1;GRIN2A,non_coding_transcript_exon_variant,,ENST00000461292,,n.3367G>A,MODIFIER,,,,-1;GRIN2A,downstream_gene_variant,,ENST00000463531,,,MODIFIER,,,,-1" "T" "ENSG00000183454" "ENST00000330684" "Transcript" "missense_variant" "missense_variant" "4276/5031" "3728/4395" "1243/1464" "G/E" "gGg/gAg" NA 1 NA -1 "GRIN2A" "HGNC" "HGNC:4585" "protein_coding" NA "CCDS10539.1" "ENSP00000332549" "Q12879" "Q547U9" "UPI000000D7AB" "NM_001134407.1" "deleterious(0)" "probably_damaging(0.994)" "13/13" NA "Pfam_domain:PF10565" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "MODERATE" NA "SNV" 1 NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "GGTTCCCCATC" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" NA TRUE "Unknown"
"64" "PDXDC1" 23042 "BI" "GRCh38" "chr16" 15009718 15009718 "+" "Missense_Mutation" "SNP" "T" "T" "C" "rs780031901" "byFrequency" "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.686T>C" "p.Ile229Thr" "p.I229T" "ENST00000396410" "8/23" 442 410 31 518 NA NA "PDXDC1,missense_variant,p.I229T,ENST00000396410,NM_015027.3,c.686T>C,MODERATE,YES,tolerated(0.24),benign(0.056),1;PDXDC1,missense_variant,p.I138T,ENST00000450288,NM_001285448.1,c.413T>C,MODERATE,,tolerated(0.37),benign(0.043),1;PDXDC1,missense_variant,p.I202T,ENST00000569715,NM_001285444.1,c.605T>C,MODERATE,,tolerated(0.15),benign(0.025),1;PDXDC1,missense_variant,p.I247T,ENST00000563679,NM_001285447.1,c.740T>C,MODERATE,,tolerated(0.38),benign(0.055),1;PDXDC1,missense_variant,p.I201T,ENST00000627450,NM_001285445.1,c.602T>C,MODERATE,,tolerated(0.15),benign(0.043),1;PDXDC1,missense_variant,p.I206T,ENST00000455313,NM_001285450.1,c.617T>C,MODERATE,,tolerated(0.13),benign(0.015),1;PDXDC1,missense_variant,p.I229T,ENST00000535621,NM_001285449.1,c.686T>C,MODERATE,,tolerated(0.27),benign(0.026),1;PDXDC1,missense_variant,p.I229T,ENST00000325823,,c.686T>C,MODERATE,,tolerated(0.28),benign(0.005),1;PDXDC1,missense_variant,p.I191T,ENST00000567306,,c.572T>C,MODERATE,,tolerated(0.18),benign(0.015),1;PDXDC1,downstream_gene_variant,,ENST00000563522,,,MODIFIER,,,,1;PDXDC1,downstream_gene_variant,,ENST00000563667,,,MODIFIER,,,,1;MIR1972-1,downstream_gene_variant,,ENST00000459337,,,MODIFIER,YES,,,-1;PDXDC1,non_coding_transcript_exon_variant,,ENST00000570001,,n.781T>C,MODIFIER,,,,1;PDXDC1,non_coding_transcript_exon_variant,,ENST00000561930,,n.408T>C,MODIFIER,,,,1;PDXDC1,intron_variant,,ENST00000562119,,c.174+7930T>C,MODIFIER,,,,1;PDXDC1,downstream_gene_variant,,ENST00000565362,,,MODIFIER,,,,1" "C" "ENSG00000179889" "ENST00000396410" "Transcript" "missense_variant" "missense_variant" "783/4521" "686/2367" "229/788" "I/T" "aTa/aCa" "rs780031901" 1 NA 1 "PDXDC1" "HGNC" "HGNC:28995" "protein_coding" "YES" "CCDS32393.1" "ENSP00000379691" "Q6P996" NA "UPI000004A864" "NM_015027.3" "tolerated(0.24)" "benign(0.056)" "8/23" NA "Pfam_domain:PF00282;Superfamily_domains:SSF53383" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "MODERATE" 1 "SNV" 1 NA NA 1 5.766e-05 5.78e-05 0 0 0.0001158 0 7.496e-05 0 6.064e-05 NA "PASS" "TGATATAGAGC" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" NA TRUE "Unknown"
"65" "UMOD" 7369 "BI" "GRCh38" "chr16" 20346185 20346185 "+" "Missense_Mutation" "SNP" "G" "G" "A" "rs373609971" "byCluster;byFrequency" "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.1123C>T" "p.Arg375Trp" "p.R375W" "ENST00000302509" "5/11" 41 28 13 64 NA NA "UMOD,missense_variant,p.R375W,ENST00000302509,NM_003361.3&NM_001008389.2,c.1123C>T,MODERATE,,deleterious(0),probably_damaging(0.956),-1;UMOD,missense_variant,p.R408W,ENST00000396134,NM_001278614.1,c.1222C>T,MODERATE,YES,deleterious(0),probably_damaging(0.939),-1;UMOD,missense_variant,p.R424W,ENST00000396138,,c.1270C>T,MODERATE,,deleterious(0),probably_damaging(0.949),-1;UMOD,missense_variant,p.R375W,ENST00000570689,,c.1123C>T,MODERATE,,deleterious(0),probably_damaging(0.956),-1;UMOD,downstream_gene_variant,,ENST00000574195,,,MODIFIER,,,,-1;UMOD,downstream_gene_variant,,ENST00000571174,,,MODIFIER,,,,-1;UMOD,downstream_gene_variant,,ENST00000577168,,,MODIFIER,,,,-1;UMOD,downstream_gene_variant,,ENST00000570972,,,MODIFIER,,,,-1;UMOD,downstream_gene_variant,,ENST00000573567,,,MODIFIER,,,,-1;UMOD,downstream_gene_variant,,ENST00000576546,,,MODIFIER,,,,-1;UMOD,downstream_gene_variant,,ENST00000570757,,,MODIFIER,,,,-1;UMOD,downstream_gene_variant,,ENST00000576688,,,MODIFIER,,,,-1;UMOD,upstream_gene_variant,,ENST00000570331,,,MODIFIER,,,,-1" "A" "ENSG00000169344" "ENST00000302509" "Transcript" "missense_variant" "missense_variant" "1415/2477" "1123/1923" "375/640" "R/W" "Cgg/Tgg" "rs373609971" 1 NA -1 "UMOD" "HGNC" "HGNC:12559" "protein_coding" NA "CCDS10583.1" "ENSP00000306279" "P07911" NA "UPI0000137E1A" "NM_003361.3;NM_001008389.2" "deleterious(0)" "probably_damaging(0.956)" "5/11" NA "Pfam_domain:PF00100;PROSITE_profiles:PS51034;SMART_domains:SM00241" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "MODERATE" NA "SNV" 5 NA NA 1 1.647e-05 1.653e-05 0 0 0 0 3.009e-05 0 0 NA "PASS" "GTCCCGGTTGT" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "gdc_pon;wga_pair" "COSM5143939;COSM5143940" TRUE "Unknown"
"66" "SLC5A11" 115584 "BI" "GRCh38" "chr16" 24884112 24884112 "+" "Silent" "SNP" "G" "G" "A" "rs759987745" NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.645G>A" "p.=" "p.A215A" "ENST00000347898" "8/16" 216 118 97 83 NA NA "SLC5A11,synonymous_variant,p.A215A,ENST00000347898,NM_052944.4,c.645G>A,LOW,YES,,,1;SLC5A11,synonymous_variant,p.A180A,ENST00000424767,NM_001258411.2,c.540G>A,LOW,,,,1;SLC5A11,synonymous_variant,p.A145A,ENST00000545376,NM_001258412.2,c.435G>A,LOW,,,,1;SLC5A11,synonymous_variant,p.A180A,ENST00000567758,,c.540G>A,LOW,,,,1;SLC5A11,synonymous_variant,p.A151A,ENST00000565769,NM_001258413.2,c.453G>A,LOW,,,,1;SLC5A11,synonymous_variant,p.A145A,ENST00000568579,,c.435G>A,LOW,,,,1;SLC5A11,synonymous_variant,p.A151A,ENST00000449109,NM_001258414.1,c.453G>A,LOW,,,,1;SLC5A11,synonymous_variant,p.A151A,ENST00000569071,,c.453G>A,LOW,,,,1;SLC5A11,3_prime_UTR_variant,,ENST00000488922,,c.*657G>A,MODIFIER,,,,1;SLC5A11,non_coding_transcript_exon_variant,,ENST00000565586,,n.322G>A,MODIFIER,,,,1" "A" "ENSG00000158865" "ENST00000347898" "Transcript" "synonymous_variant" "synonymous_variant" "1267/2745" "645/2028" "215/675" "A" "gcG/gcA" "rs759987745" 1 NA 1 "SLC5A11" "HGNC" "HGNC:23091" "protein_coding" "YES" "CCDS10625.1" "ENSP00000289932" "Q8WWX8" NA NA "NM_052944.4" NA NA "8/16" NA "Pfam_domain:PF00474;Transmembrane_helices:Tmhmm;TIGRFAM_domain:TIGR00813;PROSITE_profiles:PS50283" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "LOW" 1 "SNV" 1 NA NA 1 8.236e-06 8.262e-06 0 0 0.0001158 0 0 0 0 NA "PASS" "GGAGCGCTCAC" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" NA TRUE "Unknown"
"67" "TBX6" 6911 "BI" "GRCh38" "chr16" 30086842 30086842 "+" "Missense_Mutation" "SNP" "G" "G" "T" "novel" NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.849C>A" "p.Asp283Glu" "p.D283E" "ENST00000279386" "6/8" 111 84 27 75 NA NA "TBX6,missense_variant,p.D283E,ENST00000395224,NM_004608.3,c.849C>A,MODERATE,YES,tolerated(0.37),benign(0.004),-1;TBX6,missense_variant,p.D283E,ENST00000627355,,c.849C>A,MODERATE,,tolerated(0.25),benign(0.024),-1;TBX6,missense_variant,p.D283E,ENST00000279386,,c.849C>A,MODERATE,,tolerated(0.37),benign(0.004),-1;TBX6,downstream_gene_variant,,ENST00000553607,,,MODIFIER,,,,-1;PPP4C,downstream_gene_variant,,ENST00000279387,NM_002720.1&NM_001303503.1,,MODIFIER,YES,,,1;PPP4C,downstream_gene_variant,,ENST00000561610,,,MODIFIER,,,,1;PPP4C,downstream_gene_variant,,ENST00000627746,NM_001303507.1,,MODIFIER,,,,1;PPP4C,downstream_gene_variant,,ENST00000562664,,,MODIFIER,,,,1;PPP4C,downstream_gene_variant,,ENST00000562222,,,MODIFIER,,,,1;TBX6,intron_variant,,ENST00000567664,,c.*48-147C>A,MODIFIER,,,,-1;PPP4C,downstream_gene_variant,,ENST00000566749,,,MODIFIER,,,,1;PPP4C,downstream_gene_variant,,ENST00000563200,,,MODIFIER,,,,1;PPP4C,downstream_gene_variant,,ENST00000564966,,,MODIFIER,,,,1;PPP4C,downstream_gene_variant,,ENST00000568810,,,MODIFIER,,,,1;PPP4C,downstream_gene_variant,,ENST00000567040,,,MODIFIER,,,,1;PPP4C,downstream_gene_variant,,ENST00000563732,,,MODIFIER,,,,1;PPP4C,downstream_gene_variant,,ENST00000563597,,,MODIFIER,,,,1;PPP4C,downstream_gene_variant,,ENST00000567828,,,MODIFIER,,,,1" "T" "ENSG00000149922" "ENST00000279386" "Transcript" "missense_variant" "missense_variant" "905/1796" "849/1311" "283/436" "D/E" "gaC/gaA" NA 1 NA -1 "TBX6" "HGNC" "HGNC:11605" "protein_coding" NA "CCDS10670.1" "ENSP00000279386" "O95947" NA "UPI000013DBC7" NA "tolerated(0.37)" "benign(0.004)" "6/8" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "MODERATE" NA "SNV" 1 NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "CGGGCGTCTCG" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" NA TRUE "Unknown"
"68" "CDH11" 1009 "BI" "GRCh38" "chr16" 64951006 64951006 "+" "Missense_Mutation" "SNP" "C" "C" "T" "novel" NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.1655G>A" "p.Gly552Asp" "p.G552D" "ENST00000268603" "12/13" 94 55 39 102 NA NA "CDH11,missense_variant,p.G552D,ENST00000394156,,c.1655G>A,MODERATE,,tolerated(0.16),benign(0.346),-1;CDH11,missense_variant,p.G552D,ENST00000268603,NM_001797.2,c.1655G>A,MODERATE,YES,tolerated(0.22),benign(0.122),-1;CDH11,missense_variant,p.G426D,ENST00000566827,,c.1277G>A,MODERATE,,tolerated(0.3),benign(0.122),-1" "T" "ENSG00000140937" "ENST00000268603" "Transcript" "missense_variant" "missense_variant" "2271/6857" "1655/2391" "552/796" "G/D" "gGc/gAc" NA 1 NA -1 "CDH11" "HGNC" "HGNC:1750" "protein_coding" "YES" "CCDS10803.1" "ENSP00000268603" "P55287" NA "UPI000013D7C5" "NM_001797.2" "tolerated(0.22)" "benign(0.122)" "12/13" NA "PROSITE_profiles:PS50268;SMART_domains:SM00112;Superfamily_domains:SSF49313" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "MODERATE" 1 "SNV" 1 NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "ACACGCCTGCT" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" NA TRUE "Unknown"
"69" "BPTF" 2186 "BI" "GRCh38" "chr17" 67912428 67912428 "+" "Missense_Mutation" "SNP" "C" "C" "T" "novel" NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.4922C>T" "p.Thr1641Met" "p.T1641M" "ENST00000321892" "13/30" 152 80 71 313 NA NA "BPTF,missense_variant,p.T1641M,ENST00000321892,NM_004459.6,c.4922C>T,MODERATE,,,benign(0.416),1;BPTF,missense_variant,p.T1515M,ENST00000306378,NM_182641.3,c.4544C>T,MODERATE,YES,,possibly_damaging(0.52),1;BPTF,missense_variant,p.T1502M,ENST00000424123,,c.4505C>T,MODERATE,,,benign(0.439),1;BPTF,missense_variant,p.T1578M,ENST00000544778,,c.4733C>T,MODERATE,,,possibly_damaging(0.472),1" "T" "ENSG00000171634" "ENST00000321892" "Transcript" "missense_variant" "missense_variant" "4983/11292" "4922/9141" "1641/3046" "T/M" "aCg/aTg" NA 1 NA 1 "BPTF" "HGNC" "HGNC:3581" "protein_coding" NA NA "ENSP00000315454" "Q12830" NA "UPI0001838807" "NM_004459.6" NA "benign(0.416)" "13/30" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "MODERATE" NA "SNV" 5 NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "ACAGACGACCA" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" NA TRUE "Unknown"
"70" "ABCA6" 23460 "BI" "GRCh38" "chr17" 69112260 69112260 "+" "Silent" "SNP" "G" "G" "T" "novel" NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.2055C>A" "p.=" "p.I685I" "ENST00000284425" "16/39" 423 346 77 477 NA NA "ABCA6,synonymous_variant,p.I685I,ENST00000284425,NM_080284.2,c.2055C>A,LOW,YES,,,-1;ABCA6,downstream_gene_variant,,ENST00000592493,,,MODIFIER,,,,-1;ABCA6,non_coding_transcript_exon_variant,,ENST00000590311,,n.1721C>A,MODIFIER,,,,-1;ABCA6,non_coding_transcript_exon_variant,,ENST00000589803,,n.651C>A,MODIFIER,,,,-1" "T" "ENSG00000154262" "ENST00000284425" "Transcript" "synonymous_variant" "synonymous_variant" "2230/5300" "2055/4854" "685/1617" "I" "atC/atA" NA 1 NA -1 "ABCA6" "HGNC" "HGNC:36" "protein_coding" "YES" "CCDS11683.1" "ENSP00000284425" "Q8N139" NA "UPI000013DD9D" "NM_080284.2" NA NA "16/39" NA "PROSITE_profiles:PS50893;SMART_domains:SM00382;Superfamily_domains:SSF52540" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "LOW" 1 "SNV" 1 NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "GACATGATCAC" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" NA TRUE "Unknown"
"71" "MRPL4" 51073 "BI" "GRCh38" "chr19" 10258491 10258491 "+" "Missense_Mutation" "SNP" "C" "C" "T" "rs372183483" "by1000G;byCluster" "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.631C>T" "p.Arg211Cys" "p.R211C" "ENST00000253099" "7/9" 61 32 29 72 NA NA "MRPL4,missense_variant,p.R211C,ENST00000393733,,c.631C>T,MODERATE,,tolerated(0.08),benign(0.027),1;MRPL4,missense_variant,p.R211C,ENST00000253099,NM_015956.2,c.631C>T,MODERATE,YES,tolerated(0.19),benign(0.012),1;MRPL4,missense_variant,p.R211C,ENST00000590669,NM_146388.1,c.631C>T,MODERATE,,tolerated(0.19),benign(0.011),1;MRPL4,missense_variant,p.R211C,ENST00000307422,NM_146387.1,c.631C>T,MODERATE,,tolerated(0.19),benign(0.012),1;MRPL4,missense_variant,p.R211C,ENST00000592514,,c.631C>T,MODERATE,,tolerated(0.19),benign(0.012),1;MRPL4,missense_variant,p.R109C,ENST00000590702,,c.325C>T,MODERATE,,tolerated(0.19),benign(0.012),1;MRPL4,missense_variant,p.R210C,ENST00000588502,,c.628C>T,MODERATE,,tolerated(0.18),benign(0.011),1;MRPL4,downstream_gene_variant,,ENST00000590150,,,MODIFIER,,,,1;CTD-2369P2.5,intron_variant,,ENST00000592893,,n.358+1721G>A,MODIFIER,YES,,,-1;CTD-2369P2.4,downstream_gene_variant,,ENST00000587088,,,MODIFIER,YES,,,-1;MRPL4,3_prime_UTR_variant,,ENST00000591054,,c.*129C>T,MODIFIER,,,,1;MRPL4,downstream_gene_variant,,ENST00000592071,,,MODIFIER,,,,1" "T" "ENSG00000105364" "ENST00000253099" "Transcript" "missense_variant" "missense_variant" "918/1455" "631/936" "211/311" "R/C" "Cgc/Tgc" "rs372183483" 1 NA 1 "MRPL4" "HGNC" "HGNC:14276" "protein_coding" "YES" "CCDS12230.1" "ENSP00000253099" "Q9BYD3" "A0A024R7C5" "UPI0000072264" "NM_015956.2" "tolerated(0.19)" "benign(0.012)" "7/9" NA "Pfam_domain:PF00573;TIGRFAM_domain:TIGR03953;Superfamily_domains:SSF52166" 2e-04 0 0 NA 0 0 0.001 0 1e-04 NA NA NA NA NA NA NA "MODERATE" 1 "SNV" 1 NA NA 1 4.942e-05 4.945e-05 0 0 0 0 5.999e-05 0 0.0001211 NA "PASS" "ACCGCCGCTGG" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" NA TRUE "Unknown"
"72" "LILRA2" 11027 "BI" "GRCh38" "chr19" 54575452 54575452 "+" "Silent" "SNP" "T" "T" "C" "novel" NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.852T>C" "p.=" "p.P284P" "ENST00000251377" "6/9" 48 28 20 115 NA NA "LILRA2,synonymous_variant,p.P284P,ENST00000251376,NM_006866.2,c.852T>C,LOW,,,,1;LILRA2,synonymous_variant,p.P284P,ENST00000251377,,c.852T>C,LOW,YES,,,1;LILRA2,synonymous_variant,p.P284P,ENST00000391738,NM_001130917.1,c.852T>C,LOW,,,,1;LILRA2,synonymous_variant,p.P284P,ENST00000439534,,c.852T>C,LOW,,,,1;LILRA2,synonymous_variant,p.P272P,ENST00000391737,NM_001290270.1,c.816T>C,LOW,,,,1;LILRA1,intron_variant,,ENST00000618665,,c.70+1341T>C,MODIFIER,,,,1;LILRA2,intron_variant,,ENST00000629481,,c.315-506T>C,MODIFIER,,,,1;LILRA2,upstream_gene_variant,,ENST00000472992,,,MODIFIER,,,,1;LILRA2,downstream_gene_variant,,ENST00000495786,,,MODIFIER,,,,1" "C" "ENSG00000239998" "ENST00000251377" "Transcript" "synonymous_variant" "synonymous_variant" "985/1799" "852/1452" "284/483" "P" "ccT/ccC" NA 1 NA 1 "LILRA2" "HGNC" "HGNC:6603" "protein_coding" "YES" "CCDS46179.1" "ENSP00000251377" "Q8N149" NA "UPI00034F238E" NA NA NA "6/9" NA "PROSITE_profiles:PS50835;SMART_domains:SM00409;SMART_domains:SM00408;Superfamily_domains:SSF48726;PIRSF_domain:PIRSF001979" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "LOW" 1 "SNV" 5 NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "GGCCCTGTGAG" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" NA TRUE "Unknown"
"73" "KIR3DL3" 115653 "BI" "GRCh38" "chr19" 54735868 54735868 "+" "Missense_Mutation" "SNP" "G" "G" "T" "novel" NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.1103G>T" "p.Arg368Met" "p.R368M" "ENST00000291860" "7/8" 502 439 62 730 NA NA "KIR3DL3,missense_variant,p.R368M,ENST00000291860,NM_153443.3,c.1103G>T,MODERATE,YES,tolerated(0.07),benign(0.373),1;KIR3DL1,intron_variant,,ENST00000541392,,c.34+11338G>T,MODIFIER,,,,1;KIR2DL3,intron_variant,,ENST00000434419,,c.35-3639G>T,MODIFIER,,,,1;KIR2DL3,upstream_gene_variant,,ENST00000342376,NM_015868.2,,MODIFIER,YES,,,1;CTB-61M7.1,intron_variant,,ENST00000400864,,n.35+11338G>T,MODIFIER,YES,,,1" "T" "ENSG00000242019" "ENST00000291860" "Transcript" "missense_variant" "missense_variant" "1121/1691" "1103/1233" "368/410" "R/M" "aGg/aTg" NA 1 NA 1 "KIR3DL3" "HGNC" "HGNC:16312" "protein_coding" "YES" "CCDS12903.1" "ENSP00000291860" NA "A0A0B4J1R5" "UPI00005056C3" "NM_153443.3" "tolerated(0.07)" "benign(0.373)" "7/8" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "MODERATE" 1 "SNV" 1 NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "GAACAGGGAGG" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" NA FALSE "Unknown"
"74" "TGM3" 7053 "BI" "GRCh38" "chr20" 2335184 2335184 "+" "Missense_Mutation" "SNP" "C" "C" "T" "rs781217795" "byFrequency" "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.1711C>T" "p.Arg571Trp" "p.R571W" "ENST00000381458" "11/13" 200 167 33 202 NA NA "TGM3,missense_variant,p.R571W,ENST00000381458,NM_003245.3,c.1711C>T,MODERATE,YES,deleterious(0.02),probably_damaging(0.998),1" "T" "ENSG00000125780" "ENST00000381458" "Transcript" "missense_variant" "missense_variant" "1774/2642" "1711/2082" "571/693" "R/W" "Cgg/Tgg" "rs781217795" 1 NA 1 "TGM3" "HGNC" "HGNC:11779" "protein_coding" "YES" "CCDS33435.1" "ENSP00000370867" "Q08188" NA "UPI0000136CCC" "NM_003245.3" "deleterious(0.02)" "probably_damaging(0.998)" "11/13" NA "Pfam_domain:PF00927;Superfamily_domains:SSF49309" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "MODERATE" 1 "SNV" 1 NA NA 1 1.647e-05 1.647e-05 0 0 0 0 1.499e-05 0 6.056e-05 NA "PASS" "TGATCCGGATC" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" NA TRUE "Unknown"
"75" "TMC2" 117532 "BI" "GRCh38" "chr20" 2617159 2617159 "+" "Missense_Mutation" "SNP" "G" "G" "A" NA NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.2028G>A" "p.Met676Ile" "p.M676I" "ENST00000358864" "16/20" 461 405 54 270 NA NA "TMC2,missense_variant,p.M676I,ENST00000358864,NM_080751.2,c.2028G>A,MODERATE,YES,deleterious(0),probably_damaging(0.945),1;TMC2,non_coding_transcript_exon_variant,,ENST00000496948,,n.1449G>A,MODIFIER,,,,1" "A" "ENSG00000149488" "ENST00000358864" "Transcript" "missense_variant" "missense_variant" "2043/3169" "2028/2721" "676/906" "M/I" "atG/atA" NA 1 NA 1 "TMC2" "HGNC" "HGNC:16527" "protein_coding" "YES" "CCDS13029.2" "ENSP00000351732" "Q8TDI7" NA "UPI0000246C98" "NM_080751.2" "deleterious(0)" "probably_damaging(0.945)" "16/20" NA "Pfam_domain:PF07810" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "MODERATE" 1 "SNV" 1 NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "GTGATGAGCAG" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" "COSM2887779" TRUE "Unknown"
"76" "USP25" 29761 "BI" "GRCh38" "chr21" 15877972 15877972 "+" "Silent" "SNP" "C" "C" "T" "novel" NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.2976C>T" "p.=" "p.Y992Y" "ENST00000285679" "23/24" 79 69 10 235 NA NA "USP25,synonymous_variant,p.Y1062Y,ENST00000400183,NM_001283041.1,c.3186C>T,LOW,YES,,,1;USP25,synonymous_variant,p.Y1024Y,ENST00000285681,NM_001283042.1,c.3072C>T,LOW,,,,1;USP25,synonymous_variant,p.Y992Y,ENST00000285679,NM_013396.4,c.2976C>T,LOW,,,,1;USP25,synonymous_variant,p.Y387Y,ENST00000351097,,c.1161C>T,LOW,,,,1;USP25,downstream_gene_variant,,ENST00000449491,,,MODIFIER,,,,1;USP25,non_coding_transcript_exon_variant,,ENST00000478932,,n.1977C>T,MODIFIER,,,,1" "T" "ENSG00000155313" "ENST00000285679" "Transcript" "synonymous_variant" "synonymous_variant" "3345/3973" "2976/3168" "992/1055" "Y" "taC/taT" NA 1 NA 1 "USP25" "HGNC" "HGNC:12624" "protein_coding" NA "CCDS33515.1" "ENSP00000285679" "Q9UHP3" NA "UPI000002B680" "NM_013396.4" NA NA "23/24" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "LOW" NA "SNV" 1 NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "TCCTACCTTGG" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" NA TRUE "Unknown"
"77" "CECR1" 51816 "BI" "GRCh38" "chr22" 17209545 17209545 "+" "Missense_Mutation" "SNP" "G" "G" "A" "rs777683953" "byFrequency" "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.133C>T" "p.Arg45Trp" "p.R45W" "ENST00000262607" "1/9" 182 69 111 32 NA NA "CECR1,missense_variant,p.R45W,ENST00000399837,NM_001282226.1&NM_001282225.1,c.133C>T,MODERATE,YES,deleterious(0.04),possibly_damaging(0.828),-1;CECR1,missense_variant,p.R3W,ENST00000449907,NM_001282227.1&NM_001282228.1,c.7C>T,MODERATE,,deleterious(0.02),possibly_damaging(0.828),-1;CECR1,missense_variant,p.R45W,ENST00000399839,,c.133C>T,MODERATE,,deleterious(0.04),possibly_damaging(0.828),-1;CECR1,missense_variant,p.R45W,ENST00000262607,,c.133C>T,MODERATE,,deleterious(0.04),possibly_damaging(0.828),-1;CECR1,missense_variant,p.R45W,ENST00000441548,,c.133C>T,MODERATE,,deleterious(0.03),possibly_damaging(0.828),-1;CECR1,missense_variant,p.R45W,ENST00000543038,,c.133C>T,MODERATE,,deleterious(0.03),possibly_damaging(0.828),-1;CECR1,intron_variant,,ENST00000610390,NM_001282229.1,c.-38-2255C>T,MODIFIER,,,,-1;FAM32B,upstream_gene_variant,,ENST00000344033,,,MODIFIER,YES,,,1" "A" "ENSG00000093072" "ENST00000262607" "Transcript" "missense_variant" "missense_variant" "345/3925" "133/1536" "45/511" "R/W" "Cgg/Tgg" "rs777683953" 1 NA -1 "CECR1" "HGNC" "HGNC:1839" "protein_coding" NA "CCDS13742.1" "ENSP00000262607" "Q9NZK5" NA "UPI000013D2E8" NA "deleterious(0.04)" "possibly_damaging(0.828)" "1/9" NA "Pfam_domain:PF08451;TIGRFAM_domain:TIGR01431" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "MODERATE" NA "SNV" 1 NA NA 1 4.118e-05 4.124e-05 0 8.648e-05 0 0 6e-05 0 0 NA "PASS" "CAGCCGCATCA" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" "COSM4671355" TRUE "Unknown"
"78" "APOL1" 8542 "BI" "GRCh38" "chr22" 36254956 36254956 "+" "Translation_Start_Site" "SNP" "A" "A" "T" "novel" NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.1A>T" "p.Met1?" "p.M1?" "ENST00000397278" "2/6" 284 236 48 150 NA NA "APOL1,start_lost,p.M1?,ENST00000397278,NM_003661.3,c.1A>T,HIGH,,tolerated_low_confidence(0.33),benign(0),1;APOL1,start_lost,p.M1?,ENST00000422706,NM_001136540.1,c.1A>T,HIGH,,tolerated_low_confidence(0.33),benign(0),1;APOL1,start_lost,p.M1?,ENST00000426053,NM_001136541.1,c.1A>T,HIGH,,tolerated_low_confidence(0.33),benign(0),1;APOL1,start_lost,p.M1?,ENST00000397279,,c.1A>T,HIGH,,tolerated_low_confidence(0.33),benign(0),1;APOL1,start_lost,p.M1?,ENST00000427990,,c.1A>T,HIGH,,,,1;APOL1,start_lost,p.M1?,ENST00000433768,,c.1A>T,HIGH,,tolerated_low_confidence(0.27),benign(0.018),1;APOL1,missense_variant,p.M17L,ENST00000319136,NM_145343.2,c.49A>T,MODERATE,YES,tolerated_low_confidence(0.32),benign(0),1;APOL1,missense_variant,p.M30L,ENST00000438034,,c.88A>T,MODERATE,,tolerated_low_confidence(0.79),benign(0.002),1;APOL1,start_lost,p.M1?,ENST00000422471,,c.1A>T,HIGH,,tolerated_low_confidence(0.27),benign(0.018),1;APOL1,start_lost,p.M1?,ENST00000431184,,c.1A>T,HIGH,,tolerated_low_confidence(0.33),benign(0.018),1;APOL1,start_lost,p.M1?,ENST00000439680,,c.1A>T,HIGH,,tolerated_low_confidence(0.47),unknown(0),1;APOL1,non_coding_transcript_exon_variant,,ENST00000475519,,n.261A>T,MODIFIER,,,,1" "T" "ENSG00000100342" "ENST00000397278" "Transcript" "start_lost" "start_lost" "230/2918" "1/1197" "1/398" "M/L" "Atg/Ttg" NA 1 NA 1 "APOL1" "HGNC" "HGNC:618" "protein_coding" NA "CCDS13926.1" "ENSP00000380448" "O14791" NA "UPI000013DFEA" "NM_003661.3" "tolerated_low_confidence(0.33)" "benign(0)" "2/6" NA "Cleavage_site_(Signalp):Sigp" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "HIGH" NA "SNV" 1 NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "GCGACATGGAG" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" NA TRUE "Unknown"
"79" "TLR7" 51284 "BI" "GRCh38" "chrX" 12885712 12885712 "+" "Silent" "SNP" "G" "G" "A" "rs199530355" "byCluster" "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.204G>A" "p.=" "p.T68T" "ENST00000380659" "3/3" 830 750 80 465 NA NA "TLR7,synonymous_variant,p.T68T,ENST00000380659,NM_016562.3,c.204G>A,LOW,YES,,,1" "A" "ENSG00000196664" "ENST00000380659" "Transcript" "synonymous_variant" "synonymous_variant" "343/5011" "204/3150" "68/1049" "T" "acG/acA" "rs199530355" 1 NA 1 "TLR7" "HGNC" "HGNC:15631" "protein_coding" "YES" "CCDS14151.1" "ENSP00000370034" "Q9NYK1" "B2R9N9" "UPI000004BAF6" "NM_016562.3" NA NA "3/3" NA "Low_complexity_(Seg):Seg;Superfamily_domains:SSF52058" NA NA NA NA NA NA NA 0 1e-04 NA NA NA NA NA NA NA "LOW" 1 "SNV" 1 NA NA 1 8.237e-06 1.141e-05 0 0 0 0 2.086e-05 0 0 NA "PASS" "ACCACGAACCT" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" NA TRUE "Unknown"
"80" "TLR7" 51284 "BI" "GRCh38" "chrX" 12885798 12885798 "+" "Missense_Mutation" "SNP" "G" "G" "A" "novel" NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.290G>A" "p.Arg97Lys" "p.R97K" "ENST00000380659" "3/3" 812 719 92 419 NA NA "TLR7,missense_variant,p.R97K,ENST00000380659,NM_016562.3,c.290G>A,MODERATE,YES,tolerated(0.1),benign(0.102),1" "A" "ENSG00000196664" "ENST00000380659" "Transcript" "missense_variant" "missense_variant" "429/5011" "290/3150" "97/1049" "R/K" "aGa/aAa" NA 1 NA 1 "TLR7" "HGNC" "HGNC:15631" "protein_coding" "YES" "CCDS14151.1" "ENSP00000370034" "Q9NYK1" "B2R9N9" "UPI000004BAF6" "NM_016562.3" "tolerated(0.1)" "benign(0.102)" "3/3" NA "Superfamily_domains:SSF52058" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "MODERATE" 1 "SNV" 1 NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "TTTCAGATGCA" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" NA TRUE "Unknown"
"81" "TCEAL5" 340543 "BI" "GRCh38" "chrX" 103274011 103274011 "+" "Missense_Mutation" "SNP" "G" "G" "A" "novel" NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.553C>T" "p.Arg185Trp" "p.R185W" "ENST00000372680" "3/3" 479 332 144 835 NA NA "TCEAL5,missense_variant,p.R185W,ENST00000372680,NM_001012979.2,c.553C>T,MODERATE,YES,tolerated(0.07),probably_damaging(0.995),-1" "A" "ENSG00000204065" "ENST00000372680" "Transcript" "missense_variant" "missense_variant" "848/1168" "553/621" "185/206" "R/W" "Cgg/Tgg" NA 1 NA -1 "TCEAL5" "HGNC" "HGNC:22282" "protein_coding" "YES" "CCDS35356.1" "ENSP00000361765" "Q5H9L2" NA "UPI00001998F8" "NM_001012979.2" "tolerated(0.07)" "probably_damaging(0.995)" "3/3" NA "Low_complexity_(Seg):Seg" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "MODERATE" 1 "SNV" 1 NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "ACCCCGTTGGC" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" NA TRUE "Unknown"
"82" "CT45A3" 441519 "BI" "GRCh38" "chrX" 135761669 135761669 "+" "Silent" "SNP" "C" "C" "T" "novel" NA "TCGA-19-0957-01C-01W-0643-08" "TCGA-19-0957-10A-01W-0643-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina Genome Analyzer II" "72b706e8-67f1-49a4-876a-a4517f4212dc" "6058635d-1489-4cee-85b6-34de1eeb0256" "c.477G>A" "p.=" "p.K159K" "ENST00000597510" "3/4" 1327 1315 9 940 NA NA "CT45A3,synonymous_variant,p.K159K,ENST00000597510,,c.477G>A,LOW,YES,,,-1;CT45A3,synonymous_variant,p.K159K,ENST00000598716,NM_001017435.1,c.477G>A,LOW,,,,-1" "T" "ENSG00000269096" "ENST00000597510" "Transcript" "synonymous_variant" "synonymous_variant" "477/1076" "477/570" "159/189" "K" "aaG/aaA" NA 1 NA -1 "CT45A3" "HGNC" "HGNC:33268" "protein_coding" "YES" "CCDS76030.1" "ENSP00000471418" "Q8NHU0" NA "UPI000006D8C7" NA NA NA "3/4" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "LOW" 1 "SNV" 1 NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "AATCGCTTCCT" "c2a58b8f-79a6-44bd-94f0-85f4b1c1416d" "7a533dee-3eed-4b50-b128-a38bb6a076c4" "0d3880ea-f17a-4b79-b2fc-1b2655015d71" "a589e2dc-7649-492c-9569-592698acaa6f" "wga_pair" NA FALSE "Unknown"
"83" "KIF17" 57576 "BI" "GRCh38" "chr1" 20682753 20682753 "+" "Missense_Mutation" "SNP" "G" "G" "A" "rs370565385" "byCluster;byFrequency" "TCGA-19-5951-01A-11D-1696-08" "TCGA-19-5951-10A-01D-1696-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina HiSeq 2000" "57cf584c-8c95-42ec-9cb0-707228b70010" "0de1bd85-87e3-4189-9c82-206b20e4428f" "c.2363C>T" "p.Ser788Leu" "p.S788L" "ENST00000247986" "11/15" 55 41 14 72 NA NA "KIF17,missense_variant,p.S788L,ENST00000247986,NM_020816.3,c.2363C>T,MODERATE,YES,tolerated(0.08),benign(0.386),-1;KIF17,missense_variant,p.S788L,ENST00000400463,NM_001122819.2,c.2363C>T,MODERATE,,tolerated(0.07),benign(0.368),-1;KIF17,missense_variant,p.S688L,ENST00000375044,NM_001287212.1,c.2063C>T,MODERATE,,tolerated(0.07),benign(0.386),-1;KIF17,non_coding_transcript_exon_variant,,ENST00000490034,,n.634C>T,MODIFIER,,,,-1;KIF17,non_coding_transcript_exon_variant,,ENST00000477167,,n.511C>T,MODIFIER,,,,-1;KIF17,non_coding_transcript_exon_variant,,ENST00000462858,,n.376C>T,MODIFIER,,,,-1;KIF17,non_coding_transcript_exon_variant,,ENST00000498225,,n.457C>T,MODIFIER,,,,-1" "A" "ENSG00000117245" "ENST00000247986" "Transcript" "missense_variant" "missense_variant" "2674/3969" "2363/3090" "788/1029" "S/L" "tCg/tTg" "rs370565385" 1 NA -1 "KIF17" "HGNC" "HGNC:19167" "protein_coding" "YES" "CCDS213.1" "ENSP00000247986" "Q9P2E2" NA NA "NM_020816.3" "tolerated(0.08)" "benign(0.386)" "11/15" NA NA NA NA NA NA NA NA NA 0 1e-04 NA NA NA NA NA NA NA "MODERATE" 1 "SNV" 1 NA NA 1 4.942e-05 4.946e-05 0 0 0 0 8.997e-05 0 0 NA "PASS" "CATCCGAGTTC" "dd08cc9a-1b13-4c29-84ca-6ce5dfbcf337" "5f900ce8-f028-4686-9728-242e4890f0c4" "64fadf89-ebc9-471e-a4ea-c849d013e240" "61e00782-b709-43b1-a164-ee7f89c867e4" "gdc_pon" "COSM2156655" TRUE "Unknown"
"84" "DNALI1" 7802 "BI" "GRCh38" "chr1" 37559469 37559469 "+" "Missense_Mutation" "SNP" "C" "C" "T" "rs375269116" "byCluster" "TCGA-19-5951-01A-11D-1696-08" "TCGA-19-5951-10A-01D-1696-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina HiSeq 2000" "57cf584c-8c95-42ec-9cb0-707228b70010" "0de1bd85-87e3-4189-9c82-206b20e4428f" "c.436C>T" "p.Arg146Cys" "p.R146C" "ENST00000296218" "3/6" 49 31 18 52 NA NA "DNALI1,missense_variant,p.R146C,ENST00000296218,NM_003462.3,c.436C>T,MODERATE,YES,deleterious(0),probably_damaging(1),1;DNALI1,intron_variant,,ENST00000466723,,n.224+1721C>T,MODIFIER,,,,1;DNALI1,upstream_gene_variant,,ENST00000497858,,,MODIFIER,,,,1;DNALI1,downstream_gene_variant,,ENST00000490312,,,MODIFIER,,,,1;DNALI1,upstream_gene_variant,,ENST00000467277,,,MODIFIER,,,,1;RP3-423B22.5,downstream_gene_variant,,ENST00000423216,,,MODIFIER,YES,,,1" "T" "ENSG00000163879" "ENST00000296218" "Transcript" "missense_variant" "missense_variant" "446/2649" "436/843" "146/280" "R/C" "Cgc/Tgc" "rs375269116" 1 NA 1 "DNALI1" "HGNC" "HGNC:14353" "protein_coding" "YES" "CCDS420.1" "ENSP00000296218" "O14645" NA "UPI00001D6A0B" "NM_003462.3" "deleterious(0)" "probably_damaging(1)" "3/6" NA "Pfam_domain:PF10211" NA NA NA NA NA NA NA 0 1e-04 NA NA NA NA NA NA NA "MODERATE" 1 "SNV" 1 NA NA 1 8.237e-06 8.526e-06 0 0 0 0 1.533e-05 0 0 NA "PASS" "CTGTCCGCAGG" "dd08cc9a-1b13-4c29-84ca-6ce5dfbcf337" "5f900ce8-f028-4686-9728-242e4890f0c4" "64fadf89-ebc9-471e-a4ea-c849d013e240" "61e00782-b709-43b1-a164-ee7f89c867e4" NA "COSM2156639" TRUE "Unknown"
"85" "TIE1" 7075 "BI" "GRCh38" "chr1" 43319307 43319307 "+" "Missense_Mutation" "SNP" "G" "G" "T" NA NA "TCGA-19-5951-01A-11D-1696-08" "TCGA-19-5951-10A-01D-1696-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina HiSeq 2000" "57cf584c-8c95-42ec-9cb0-707228b70010" "0de1bd85-87e3-4189-9c82-206b20e4428f" "c.2995G>T" "p.Gly999Cys" "p.G999C" "ENST00000372476" "18/23" 103 70 33 130 NA NA "TIE1,missense_variant,p.G999C,ENST00000372476,NM_001253357.1&NM_005424.4,c.2995G>T,MODERATE,YES,deleterious(0),probably_damaging(0.998),1;TIE1,non_coding_transcript_exon_variant,,ENST00000473014,,n.1624G>T,MODIFIER,,,,1;TIE1,non_coding_transcript_exon_variant,,ENST00000492599,,n.216G>T,MODIFIER,,,,1;TIE1,downstream_gene_variant,,ENST00000461061,,,MODIFIER,,,,1;TIE1,upstream_gene_variant,,ENST00000492874,,,MODIFIER,,,,1" "T" "ENSG00000066056" "ENST00000372476" "Transcript" "missense_variant" "missense_variant" "3074/3882" "2995/3417" "999/1138" "G/C" "Ggc/Tgc" NA 1 NA 1 "TIE1" "HGNC" "HGNC:11809" "protein_coding" "YES" "CCDS482.1" "ENSP00000361554" "P35590" NA "UPI0000032E59" "NM_001253357.1;NM_005424.4" "deleterious(0)" "probably_damaging(0.998)" "18/23" NA "Pfam_domain:PF07714;Pfam_domain:PF00069;PROSITE_profiles:PS50011;SMART_domains:SM00220;SMART_domains:SM00219;Superfamily_domains:SSF56112" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "MODERATE" 1 "SNV" 1 NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "ACTTCGGCCTT" "dd08cc9a-1b13-4c29-84ca-6ce5dfbcf337" "5f900ce8-f028-4686-9728-242e4890f0c4" "64fadf89-ebc9-471e-a4ea-c849d013e240" "61e00782-b709-43b1-a164-ee7f89c867e4" NA "COSM2156611" TRUE "Unknown"
"86" "LCE3A" 353142 "BI" "GRCh38" "chr1" 152622974 152622974 "+" "Missense_Mutation" "SNP" "C" "C" "T" NA NA "TCGA-19-5951-01A-11D-1696-08" "TCGA-19-5951-10A-01D-1696-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina HiSeq 2000" "57cf584c-8c95-42ec-9cb0-707228b70010" "0de1bd85-87e3-4189-9c82-206b20e4428f" "c.130G>A" "p.Glu44Lys" "p.E44K" "ENST00000335674" "1/1" 65 35 30 82 NA NA "LCE3A,missense_variant,p.E44K,ENST00000335674,NM_178431.1,c.130G>A,MODERATE,YES,deleterious_low_confidence(0.03),unknown(0),-1" "T" "ENSG00000185962" "ENST00000335674" "Transcript" "missense_variant" "missense_variant" "130/270" "130/270" "44/89" "E/K" "Gag/Aag" NA 1 NA -1 "LCE3A" "HGNC" "HGNC:29461" "protein_coding" "YES" "CCDS1017.1" "ENSP00000335006" "Q5TA76" NA "UPI00001927D2" "NM_178431.1" "deleterious_low_confidence(0.03)" "unknown(0)" "1/1" NA "Low_complexity_(Seg):Seg" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "MODERATE" 1 "SNV" NA NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "GCGCTCGGAGC" "dd08cc9a-1b13-4c29-84ca-6ce5dfbcf337" "5f900ce8-f028-4686-9728-242e4890f0c4" "64fadf89-ebc9-471e-a4ea-c849d013e240" "61e00782-b709-43b1-a164-ee7f89c867e4" NA "COSM2156605" TRUE "Unknown"
"87" "HMCN1" 83872 "BI" "GRCh38" "chr1" 186076609 186076609 "+" "Silent" "SNP" "A" "A" "G" NA NA "TCGA-19-5951-01A-11D-1696-08" "TCGA-19-5951-10A-01D-1696-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina HiSeq 2000" "57cf584c-8c95-42ec-9cb0-707228b70010" "0de1bd85-87e3-4189-9c82-206b20e4428f" "c.8472A>G" "p.=" "p.V2824V" "ENST00000271588" "54/107" 74 50 24 84 NA NA "HMCN1,synonymous_variant,p.V2824V,ENST00000271588,NM_031935.2,c.8472A>G,LOW,YES,,,1" "G" "ENSG00000143341" "ENST00000271588" "Transcript" "synonymous_variant" "synonymous_variant" "8701/18208" "8472/16908" "2824/5635" "V" "gtA/gtG" NA 1 NA 1 "HMCN1" "HGNC" "HGNC:19194" "protein_coding" "YES" "CCDS30956.1" "ENSP00000271588" "Q96RW7" NA "UPI0000458C0E" "NM_031935.2" NA NA "54/107" NA "Pfam_domain:PF07679;Pfam_domain:PF00047;PROSITE_profiles:PS50835;SMART_domains:SM00409;SMART_domains:SM00408;Superfamily_domains:SSF48726" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "LOW" 1 "SNV" 1 NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "AAAGTATTGAT" "dd08cc9a-1b13-4c29-84ca-6ce5dfbcf337" "5f900ce8-f028-4686-9728-242e4890f0c4" "64fadf89-ebc9-471e-a4ea-c849d013e240" "61e00782-b709-43b1-a164-ee7f89c867e4" NA "COSM2156668" TRUE "Unknown"
"88" "LEFTY2" 7044 "BI" "GRCh38" "chr1" 225939898 225939898 "+" "Missense_Mutation" "SNP" "G" "G" "A" "rs746371252" NA "TCGA-19-5951-01A-11D-1696-08" "TCGA-19-5951-10A-01D-1696-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina HiSeq 2000" "57cf584c-8c95-42ec-9cb0-707228b70010" "0de1bd85-87e3-4189-9c82-206b20e4428f" "c.355C>T" "p.Arg119Trp" "p.R119W" "ENST00000366820" "2/4" 15 8 7 15 NA NA "LEFTY2,missense_variant,p.R119W,ENST00000366820,NM_003240.3,c.355C>T,MODERATE,YES,deleterious(0),probably_damaging(0.959),-1;LEFTY2,missense_variant,p.R119W,ENST00000616737,,c.355C>T,MODERATE,,deleterious(0),probably_damaging(0.964),-1;LEFTY2,intron_variant,,ENST00000420304,NM_001172425.1,c.280-27C>T,MODIFIER,,,,-1;RP4-559A3.6,upstream_gene_variant,,ENST00000513672,,,MODIFIER,YES,,,-1;LEFTY2,non_coding_transcript_exon_variant,,ENST00000474493,,n.204C>T,MODIFIER,,,,-1" "A" "ENSG00000143768" "ENST00000366820" "Transcript" "missense_variant" "missense_variant" "704/2287" "355/1101" "119/366" "R/W" "Cgg/Tgg" "rs746371252" 1 NA -1 "LEFTY2" "HGNC" "HGNC:3122" "protein_coding" "YES" "CCDS1549.1" "ENSP00000355785" "O00292" "A0A024R3P5" "UPI0000136CBB" "NM_003240.3" "deleterious(0)" "probably_damaging(0.959)" "2/4" NA "Pfam_domain:PF00688;Prints_domain:PR01427;PIRSF_domain:PIRSF037402" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "MODERATE" 1 "SNV" 1 NA NA 1 9.119e-06 0 0 0 0 0 0 0 0 NA "PASS" "GAGCCGCAGCA" "dd08cc9a-1b13-4c29-84ca-6ce5dfbcf337" "5f900ce8-f028-4686-9728-242e4890f0c4" "64fadf89-ebc9-471e-a4ea-c849d013e240" "61e00782-b709-43b1-a164-ee7f89c867e4" NA "COSM3400368" TRUE "Unknown"
"89" "OR2T1" 26696 "BI" "GRCh38" "chr1" 248406614 248406614 "+" "Missense_Mutation" "SNP" "T" "T" "C" "rs373134110" "byCluster;byFrequency" "TCGA-19-5951-01A-11D-1696-08" "TCGA-19-5951-10A-01D-1696-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina HiSeq 2000" "57cf584c-8c95-42ec-9cb0-707228b70010" "0de1bd85-87e3-4189-9c82-206b20e4428f" "c.620T>C" "p.Phe207Ser" "p.F207S" "ENST00000366474" "1/1" 75 44 31 83 NA NA "OR2T1,missense_variant,p.F207S,ENST00000366474,NM_030904.1,c.620T>C,MODERATE,YES,tolerated(0.07),probably_damaging(0.994),1" "C" "ENSG00000175143" "ENST00000366474" "Transcript" "missense_variant" "missense_variant" "620/1110" "620/1110" "207/369" "F/S" "tTc/tCc" "rs373134110" 1 NA 1 "OR2T1" "HGNC" "HGNC:8277" "protein_coding" "YES" "CCDS31115.1" "ENSP00000355430" "O43869" NA "UPI00003B2872" "NM_030904.1" "tolerated(0.07)" "probably_damaging(0.994)" "1/1" NA "Pfam_domain:PF00001;Transmembrane_helices:Tmhmm;PROSITE_profiles:PS50262;Superfamily_domains:SSF81321" NA NA NA NA NA NA NA 0 1e-04 NA NA NA NA NA NA NA "MODERATE" 1 "SNV" NA NA NA 1 1.647e-05 1.648e-05 0 0 0 0 2.998e-05 0 0 NA "PASS" "TGGCTTCCTCC" "dd08cc9a-1b13-4c29-84ca-6ce5dfbcf337" "5f900ce8-f028-4686-9728-242e4890f0c4" "64fadf89-ebc9-471e-a4ea-c849d013e240" "61e00782-b709-43b1-a164-ee7f89c867e4" NA "COSM2156609" TRUE "Unknown"
"90" "FUNDC2P2" 388965 "BI" "GRCh38" "chr2" 84290753 84290753 "+" "RNA" "SNP" "C" "C" "T" "rs542561893" NA "TCGA-19-5951-01A-11D-1696-08" "TCGA-19-5951-10A-01D-1696-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina HiSeq 2000" "57cf584c-8c95-42ec-9cb0-707228b70010" "0de1bd85-87e3-4189-9c82-206b20e4428f" "n.71C>T" NA NA "ENST00000331369" "1/2" 13 5 8 11 NA NA "FUNDC2P2,non_coding_transcript_exon_variant,,ENST00000331369,,n.71C>T,MODIFIER,YES,,,1;FUNDC2P2,upstream_gene_variant,,ENST00000443452,,,MODIFIER,,,,1" "T" "ENSG00000182814" "ENST00000331369" "Transcript" "non_coding_transcript_exon_variant" "non_coding_transcript_exon_variant;non_coding_transcript_variant" "71/1223" NA NA NA NA "rs542561893" 1 NA 1 "FUNDC2P2" "HGNC" "HGNC:17247" "processed_transcript" "YES" NA NA NA NA NA NA NA NA "1/2" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "MODIFIER" 1 "SNV" 1 NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "GACAGCGCGCC" "dd08cc9a-1b13-4c29-84ca-6ce5dfbcf337" "5f900ce8-f028-4686-9728-242e4890f0c4" "64fadf89-ebc9-471e-a4ea-c849d013e240" "61e00782-b709-43b1-a164-ee7f89c867e4" NA NA TRUE "Unknown"
"91" "IGKC" 3514 "BI" "GRCh38" "chr2" 89040252 89040252 "+" "Missense_Mutation" "SNP" "T" "T" "A" "novel" NA "TCGA-19-5951-01A-11D-1696-08" "TCGA-19-5951-10A-01D-1696-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina HiSeq 2000" "57cf584c-8c95-42ec-9cb0-707228b70010" "0de1bd85-87e3-4189-9c82-206b20e4428f" "c.323A>T" "p.Tyr108Phe" "p.Y108F" "ENST00000614656" "2/4" 418 295 120 358 NA NA "IGKC,missense_variant,p.Y108F,ENST00000614656,,c.323A>T,MODERATE,YES,deleterious(0.02),possibly_damaging(0.777),-1;IGKV1-12,missense_variant,p.Y108F,ENST00000480492,,c.323A>T,MODERATE,YES,deleterious(0),probably_damaging(0.964),-1;IGKC,intron_variant,,ENST00000610638,,c.-1-20217A>T,MODIFIER,,,,-1;IGKC,intron_variant,,ENST00000614252,,c.227-30152A>T,MODIFIER,,,,-1" "A" "ENSG00000211592" "ENST00000614656" "Transcript" "missense_variant" "missense_variant" "335/824" "323/711" "108/236" "Y/F" "tAc/tTc" NA 1 NA -1 "IGKC" "HGNC" "HGNC:5716" "IG_C_gene" "YES" NA "ENSP00000478196" NA "A0A087WTX5" "UPI0000D611CE" NA "deleterious(0.02)" "possibly_damaging(0.777)" "2/4" NA "Pfam_domain:PF07686;Pfam_domain:PF07679;PROSITE_profiles:PS50835;SMART_domains:SM00409;SMART_domains:SM00406;Superfamily_domains:SSF48726" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "MODERATE" 1 "SNV" NA NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "AATAGTAAGTT" "dd08cc9a-1b13-4c29-84ca-6ce5dfbcf337" "5f900ce8-f028-4686-9728-242e4890f0c4" "64fadf89-ebc9-471e-a4ea-c849d013e240" "61e00782-b709-43b1-a164-ee7f89c867e4" NA NA FALSE "Unknown"
"92" "ITGB6" 3694 "BI" "GRCh38" "chr2" 160137462 160137462 "+" "Silent" "SNP" "G" "G" "A" "rs61737765" "by1000G;byCluster;byFrequency" "TCGA-19-5951-01A-11D-1696-08" "TCGA-19-5951-10A-01D-1696-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina HiSeq 2000" "57cf584c-8c95-42ec-9cb0-707228b70010" "0de1bd85-87e3-4189-9c82-206b20e4428f" "c.1632C>T" "p.=" "p.C544C" "ENST00000283249" "10/15" 107 64 43 98 NA NA "ITGB6,synonymous_variant,p.C544C,ENST00000283249,NM_001282353.1&NM_001282389.1&NM_000888.4,c.1632C>T,LOW,YES,,,-1;ITGB6,synonymous_variant,p.C449C,ENST00000620391,NM_001282354.1&NM_001282390.1,c.1347C>T,LOW,,,,-1;ITGB6,synonymous_variant,p.C502C,ENST00000428609,NM_001282388.1,c.1506C>T,LOW,,,,-1;ITGB6,synonymous_variant,p.C544C,ENST00000409872,,c.1632C>T,LOW,,,,-1;ITGB6,synonymous_variant,p.C544C,ENST00000409967,NM_001282355.1,c.1632C>T,LOW,,,,-1;ITGB6,downstream_gene_variant,,ENST00000485635,,,MODIFIER,,,,-1;ITGB6,3_prime_UTR_variant,,ENST00000409583,,c.*1246C>T,MODIFIER,,,,-1" "A" "ENSG00000115221" "ENST00000283249" "Transcript" "synonymous_variant" "synonymous_variant" "1870/4675" "1632/2367" "544/788" "C" "tgC/tgT" "rs61737765" 1 NA -1 "ITGB6" "HGNC" "HGNC:6161" "protein_coding" "YES" "CCDS2212.1" "ENSP00000283249" "P18564" NA "UPI000012DA13" "NM_001282353.1;NM_001282389.1;NM_000888.4" NA NA "10/15" NA "PROSITE_profiles:PS50311;Superfamily_domains:SSF57196;PIRSF_domain:PIRSF002512" 0.0016 0.0061 0 NA 0 0 0 0.0052 1e-04 NA NA NA NA NA NA NA "LOW" 1 "SNV" 1 NA NA 1 0.0004942 0.0005027 0.00558 8.648e-05 0 0 1.51e-05 0 0 NA "PASS" "CTCACGCAGGA" "dd08cc9a-1b13-4c29-84ca-6ce5dfbcf337" "5f900ce8-f028-4686-9728-242e4890f0c4" "64fadf89-ebc9-471e-a4ea-c849d013e240" "61e00782-b709-43b1-a164-ee7f89c867e4" "common_in_exac;gdc_pon" "COSM2156595" TRUE "Unknown"
"93" "COL6A3" 1293 "BI" "GRCh38" "chr2" 237367038 237367038 "+" "Missense_Mutation" "SNP" "C" "C" "T" "rs376135795" "byCluster;byFrequency" "TCGA-19-5951-01A-11D-1696-08" "TCGA-19-5951-10A-01D-1696-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina HiSeq 2000" "57cf584c-8c95-42ec-9cb0-707228b70010" "0de1bd85-87e3-4189-9c82-206b20e4428f" "c.5149G>A" "p.Ala1717Thr" "p.A1717T" "ENST00000295550" "11/44" 53 31 21 44 NA NA "COL6A3,missense_variant,p.A1717T,ENST00000295550,NM_004369.3,c.5149G>A,MODERATE,YES,,probably_damaging(0.994),-1;COL6A3,missense_variant,p.A1511T,ENST00000353578,NM_057167.3,c.4531G>A,MODERATE,,,probably_damaging(0.946),-1;COL6A3,missense_variant,p.A1511T,ENST00000409809,,c.4531G>A,MODERATE,,,probably_damaging(0.946),-1;COL6A3,missense_variant,p.A1110T,ENST00000472056,NM_057166.4,c.3328G>A,MODERATE,,tolerated(0.07),unknown(0),-1;COL6A3,missense_variant,p.A1110T,ENST00000347401,,c.3328G>A,MODERATE,,tolerated(0.07),unknown(0),-1;COL6A3,downstream_gene_variant,,ENST00000392004,NM_057165.4,,MODIFIER,,,,-1;COL6A3,downstream_gene_variant,,ENST00000392003,NM_057164.4,,MODIFIER,,,,-1" "T" "ENSG00000163359" "ENST00000295550" "Transcript" "missense_variant" "missense_variant" "5602/10749" "5149/9534" "1717/3177" "A/T" "Gcc/Acc" "rs376135795" 1 NA -1 "COL6A3" "HGNC" "HGNC:2213" "protein_coding" "YES" "CCDS33412.1" "ENSP00000295550" "P12111" "D9ZGF2" NA "NM_004369.3" NA "probably_damaging(0.994)" "11/44" NA "Pfam_domain:PF00092;PROSITE_profiles:PS50234;SMART_domains:SM00327;Superfamily_domains:SSF53300" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "MODERATE" 1 "SNV" 1 NA NA 1 8.236e-06 8.244e-06 0 0 0 0 0 0 6.069e-05 NA "PASS" "GTTGGCGTGTC" "dd08cc9a-1b13-4c29-84ca-6ce5dfbcf337" "5f900ce8-f028-4686-9728-242e4890f0c4" "64fadf89-ebc9-471e-a4ea-c849d013e240" "61e00782-b709-43b1-a164-ee7f89c867e4" NA "COSM2156588" TRUE "Unknown"
"94" "BSN" 8927 "BI" "GRCh38" "chr3" 49651751 49651751 "+" "Missense_Mutation" "SNP" "G" "G" "A" "rs376181418" "byCluster;byFrequency" "TCGA-19-5951-01A-11D-1696-08" "TCGA-19-5951-10A-01D-1696-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina HiSeq 2000" "57cf584c-8c95-42ec-9cb0-707228b70010" "0de1bd85-87e3-4189-9c82-206b20e4428f" "c.2195G>A" "p.Arg732Gln" "p.R732Q" "ENST00000296452" "5/12" 70 43 27 99 NA NA "BSN,missense_variant,p.R732Q,ENST00000296452,NM_003458.3,c.2195G>A,MODERATE,YES,,unknown(0),1;BSN,downstream_gene_variant,,ENST00000467456,,,MODIFIER,,,,1" "A" "ENSG00000164061" "ENST00000296452" "Transcript" "missense_variant" "missense_variant" "2309/15955" "2195/11781" "732/3926" "R/Q" "cGg/cAg" "rs376181418" 1 NA 1 "BSN" "HGNC" "HGNC:1117" "protein_coding" "YES" "CCDS2800.1" "ENSP00000296452" "Q9UPA5" NA "UPI000013E33C" "NM_003458.3" NA "unknown(0)" "5/12" NA NA NA NA NA NA NA NA NA 0 1e-04 NA NA NA NA NA NA NA "MODERATE" 1 "SNV" 1 NA NA 1 4.118e-05 4.164e-05 0 0.0001735 0 0 4.556e-05 0 0 NA "PASS" "CATGCGGCCTT" "dd08cc9a-1b13-4c29-84ca-6ce5dfbcf337" "5f900ce8-f028-4686-9728-242e4890f0c4" "64fadf89-ebc9-471e-a4ea-c849d013e240" "61e00782-b709-43b1-a164-ee7f89c867e4" NA "COSM2156650" TRUE "Unknown"
"95" "SEMA3G" 56920 "BI" "GRCh38" "chr3" 52441273 52441273 "+" "Silent" "SNP" "G" "G" "A" "rs138050174" NA "TCGA-19-5951-01A-11D-1696-08" "TCGA-19-5951-10A-01D-1696-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina HiSeq 2000" "57cf584c-8c95-42ec-9cb0-707228b70010" "0de1bd85-87e3-4189-9c82-206b20e4428f" "c.804C>T" "p.=" "p.R268R" "ENST00000231721" "7/16" 71 42 29 103 NA NA "SEMA3G,synonymous_variant,p.R268R,ENST00000231721,NM_020163.1,c.804C>T,LOW,YES,,,-1;SEMA3G,downstream_gene_variant,,ENST00000475739,,,MODIFIER,,,,-1;SEMA3G,3_prime_UTR_variant,,ENST00000465657,,c.*223C>T,MODIFIER,,,,-1" "A" "ENSG00000010319" "ENST00000231721" "Transcript" "synonymous_variant" "synonymous_variant" "804/4899" "804/2349" "268/782" "R" "cgC/cgT" "rs138050174" 1 NA -1 "SEMA3G" "HGNC" "HGNC:30400" "protein_coding" "YES" "CCDS2856.1" "ENSP00000231721" "Q9NS98" NA "UPI000004250D" "NM_020163.1" NA NA "7/16" NA "Pfam_domain:PF01403;PROSITE_profiles:PS51004;SMART_domains:SM00630;Superfamily_domains:SSF101912" NA NA NA NA NA NA NA 2e-04 0 NA NA NA NA NA NA NA "LOW" 1 "SNV" 1 NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "CAGACGCGGCC" "dd08cc9a-1b13-4c29-84ca-6ce5dfbcf337" "5f900ce8-f028-4686-9728-242e4890f0c4" "64fadf89-ebc9-471e-a4ea-c849d013e240" "61e00782-b709-43b1-a164-ee7f89c867e4" NA "COSM2156643" TRUE "Unknown"
"96" "PLXNA1" 5361 "BI" "GRCh38" "chr3" 127014596 127014596 "+" "Missense_Mutation" "SNP" "G" "G" "A" "rs138171477" NA "TCGA-19-5951-01A-11D-1696-08" "TCGA-19-5951-10A-01D-1696-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina HiSeq 2000" "57cf584c-8c95-42ec-9cb0-707228b70010" "0de1bd85-87e3-4189-9c82-206b20e4428f" "c.2723G>A" "p.Ser908Asn" "p.S908N" "ENST00000393409" "12/31" 141 82 59 116 NA NA "PLXNA1,missense_variant,p.S908N,ENST00000393409,NM_032242.3,c.2723G>A,MODERATE,YES,tolerated(0.86),benign(0.002),1" "A" "ENSG00000114554" "ENST00000393409" "Transcript" "missense_variant" "missense_variant" "2723/9066" "2723/5691" "908/1896" "S/N" "aGc/aAc" "rs138171477" 1 NA 1 "PLXNA1" "HGNC" "HGNC:9099" "protein_coding" "YES" "CCDS33847.2" "ENSP00000377061" "Q9UIW2" NA "UPI00001A7983" "NM_032242.3" "tolerated(0.86)" "benign(0.002)" "12/31" NA "Pfam_domain:PF01833;SMART_domains:SM00429;Superfamily_domains:SSF81296" NA NA NA NA NA NA NA 0 1e-04 NA NA NA NA NA NA NA "MODERATE" 1 "SNV" 1 NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "GTGCAGCCCTG" "dd08cc9a-1b13-4c29-84ca-6ce5dfbcf337" "5f900ce8-f028-4686-9728-242e4890f0c4" "64fadf89-ebc9-471e-a4ea-c849d013e240" "61e00782-b709-43b1-a164-ee7f89c867e4" NA "COSM2156656" TRUE "Unknown"
"97" "D4S234E" 27065 "BI" "GRCh38" "chr4" 4409593 4409593 "+" "Silent" "SNP" "C" "C" "T" "rs143847165" "byCluster" "TCGA-19-5951-01A-11D-1696-08" "TCGA-19-5951-10A-01D-1696-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina HiSeq 2000" "57cf584c-8c95-42ec-9cb0-707228b70010" "0de1bd85-87e3-4189-9c82-206b20e4428f" "c.267C>T" "p.=" "p.F89F" "ENST00000433139" "4/5" 84 44 40 101 NA NA "D4S234E,synonymous_variant,p.F89F,ENST00000421177,,c.267C>T,LOW,YES,,,1;D4S234E,synonymous_variant,p.F89F,ENST00000513555,,c.267C>T,LOW,,,,1;D4S234E,synonymous_variant,p.F89F,ENST00000397958,NM_001287763.1,c.267C>T,LOW,,,,1;D4S234E,synonymous_variant,p.F89F,ENST00000433139,NM_001040101.1&NM_001287764.1,c.267C>T,LOW,,,,1;D4S234E,synonymous_variant,p.F89F,ENST00000621129,NM_014392.4,c.267C>T,LOW,,,,1;D4S234E,synonymous_variant,p.F50F,ENST00000504171,,c.150C>T,LOW,,,,1;D4S234E,synonymous_variant,p.F89F,ENST00000505246,,c.267C>T,LOW,,,,1;D4S234E,synonymous_variant,p.F89F,ENST00000506380,,c.267C>T,LOW,,,,1;D4S234E,synonymous_variant,p.F89F,ENST00000513829,,c.267C>T,LOW,,,,1" "T" "ENSG00000168824" "ENST00000433139" "Transcript" "synonymous_variant" "synonymous_variant" "399/2254" "267/558" "89/185" "F" "ttC/ttT" "rs143847165" 1 NA 1 "D4S234E" "Uniprot_gn" NA "protein_coding" NA "CCDS3376.1" "ENSP00000408833" "P42857" "B2R5R8" "UPI0000130549" "NM_001040101.1;NM_001287764.1" NA NA "4/5" NA "Low_complexity_(Seg):Seg;Pfam_domain:PF06387;Transmembrane_helices:Tmhmm;PIRSF_domain:PIRSF002383" NA NA NA NA NA NA NA 0 1e-04 NA NA NA NA NA NA NA "LOW" NA "SNV" 2 NA NA 1 7.413e-05 7.419e-05 0 8.645e-05 0.0008091 0 1.5e-05 0 0 NA "PASS" "CTCTTCGCCCT" "dd08cc9a-1b13-4c29-84ca-6ce5dfbcf337" "5f900ce8-f028-4686-9728-242e4890f0c4" "64fadf89-ebc9-471e-a4ea-c849d013e240" "61e00782-b709-43b1-a164-ee7f89c867e4" "common_in_exac" "COSM2156610" TRUE "Unknown"
"98" "UGT2A3" 79799 "BI" "GRCh38" "chr4" 68929997 68929997 "+" "Missense_Mutation" "SNP" "C" "C" "T" "rs553189244" "byCluster;byFrequency" "TCGA-19-5951-01A-11D-1696-08" "TCGA-19-5951-10A-01D-1696-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina HiSeq 2000" "57cf584c-8c95-42ec-9cb0-707228b70010" "0de1bd85-87e3-4189-9c82-206b20e4428f" "c.1400G>A" "p.Arg467His" "p.R467H" "ENST00000251566" "6/6" 129 69 59 150 NA NA "UGT2A3,missense_variant,p.R467H,ENST00000251566,NM_024743.3,c.1400G>A,MODERATE,YES,tolerated(0.05),benign(0.103),-1;UGT2A3,3_prime_UTR_variant,,ENST00000503012,,c.*576G>A,MODIFIER,,,,-1" "T" "ENSG00000135220" "ENST00000251566" "Transcript" "missense_variant" "missense_variant" "1431/2965" "1400/1584" "467/527" "R/H" "cGc/cAc" "rs553189244" 1 NA -1 "UGT2A3" "HGNC" "HGNC:28528" "protein_coding" "YES" "CCDS3525.1" "ENSP00000251566" "Q6UWM9" NA "UPI000004E644" "NM_024743.3" "tolerated(0.05)" "benign(0.103)" "6/6" NA "Pfam_domain:PF00201;Superfamily_domains:SSF53756" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "MODERATE" 1 "SNV" 1 NA NA 1 6.589e-05 6.596e-05 0 0 0.0001157 0 5.998e-05 0 0.0001817 NA "PASS" "TGTGGCGCATG" "dd08cc9a-1b13-4c29-84ca-6ce5dfbcf337" "5f900ce8-f028-4686-9728-242e4890f0c4" "64fadf89-ebc9-471e-a4ea-c849d013e240" "61e00782-b709-43b1-a164-ee7f89c867e4" "gdc_pon" "COSM2156649" TRUE "Unknown"
"99" "FAT4" 79633 "BI" "GRCh38" "chr4" 125320214 125320214 "+" "Missense_Mutation" "SNP" "C" "C" "T" NA NA "TCGA-19-5951-01A-11D-1696-08" "TCGA-19-5951-10A-01D-1696-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina HiSeq 2000" "57cf584c-8c95-42ec-9cb0-707228b70010" "0de1bd85-87e3-4189-9c82-206b20e4428f" "c.3803C>T" "p.Thr1268Ile" "p.T1268I" "ENST00000394329" "1/17" 117 90 27 114 NA NA "FAT4,missense_variant,p.T1268I,ENST00000394329,NM_024582.4&NM_001291303.1&NM_001291285.1,c.3803C>T,MODERATE,YES,,benign(0.033),1" "T" "ENSG00000196159" "ENST00000394329" "Transcript" "missense_variant" "missense_variant" "3816/16123" "3803/14946" "1268/4981" "T/I" "aCa/aTa" NA 1 NA 1 "FAT4" "HGNC" "HGNC:23109" "protein_coding" "YES" "CCDS3732.3" "ENSP00000377862" "Q6V0I7" NA "UPI000155D6E3" "NM_024582.4;NM_001291303.1;NM_001291285.1" NA "benign(0.033)" "1/17" NA "Pfam_domain:PF00028;PROSITE_profiles:PS50268;SMART_domains:SM00112;Superfamily_domains:SSF49313" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "MODERATE" 1 "SNV" 5 NA NA 1 NA NA NA NA NA NA NA NA NA NA "PASS" "GGTAACACTAA" "dd08cc9a-1b13-4c29-84ca-6ce5dfbcf337" "5f900ce8-f028-4686-9728-242e4890f0c4" "64fadf89-ebc9-471e-a4ea-c849d013e240" "61e00782-b709-43b1-a164-ee7f89c867e4" NA "COSM2156657;COSM2156658" TRUE "Unknown"
"100" "INPP4B" 8821 "BI" "GRCh38" "chr4" 142237952 142237952 "+" "Nonsense_Mutation" "SNP" "G" "G" "A" "rs763155133" "byFrequency" "TCGA-19-5951-01A-11D-1696-08" "TCGA-19-5951-10A-01D-1696-08" NA NA NA NA NA NA NA NA "Somatic" NA NA NA NA NA "Illumina HiSeq 2000" "57cf584c-8c95-42ec-9cb0-707228b70010" "0de1bd85-87e3-4189-9c82-206b20e4428f" "c.748C>T" "p.Arg250Ter" "p.R250*" "ENST00000262992" "10/24" 44 26 18 64 NA NA "INPP4B,stop_gained,p.R250*,ENST00000513000,NM_003866.2,c.748C>T,HIGH,YES,,,-1;INPP4B,stop_gained,p.R250*,ENST00000509777,,c.748C>T,HIGH,,,,-1;INPP4B,stop_gained,p.R250*,ENST00000262992,NM_001101669.1,c.748C>T,HIGH,,,,-1;INPP4B,stop_gained,p.R250*,ENST00000508116,,c.748C>T,HIGH,,,,-1;INPP4B,stop_gained,p.R250*,ENST00000510812,,c.748C>T,HIGH,,,,-1;INPP4B,stop_gained,p.R65*,ENST00000511838,,c.193C>T,HIGH,,,,-1;INPP4B,stop_gained,p.R121*,ENST00000514525,,c.361C>T,HIGH,,,,-1;INPP4B,stop_gained,p.R250*,ENST00000512630,,c.748C>T,HIGH,,,,-1;INPP4B,3_prime_UTR_variant,,ENST00000506297,,c.*529C>T,MODIFIER,,,,-1" "A" "ENSG00000109452" "ENST00000262992" "Transcript" "stop_gained" "stop_gained" "965/3741" "748/2775" "250/924" "R/*" "Cga/Tga" "rs763155133" 1 NA -1 "INPP4B" "HGNC" "HGNC:6075" "protein_coding" NA "CCDS3757.1" "ENSP00000262992" "O15327" NA "UPI000013D37A" "NM_001101669.1" NA NA "10/24" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "HIGH" NA "SNV" 1 NA NA 1 1.648e-05 1.675e-05 9.915e-05 0 0 0 1.525e-05 0 0 NA "PASS" "AATTCGCATCC" "dd08cc9a-1b13-4c29-84ca-6ce5dfbcf337" "5f900ce8-f028-4686-9728-242e4890f0c4" "64fadf89-ebc9-471e-a4ea-c849d013e240" "61e00782-b709-43b1-a164-ee7f89c867e4" NA "COSM1051543;COSM4329861;COSM4867560" TRUE "Unknown"
