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,DISTANCE,TRANSCRIPT_STRAND,SYMBOL,SYMBOL_SOURCE,HGNC_ID,BIOTYPE,CANONICAL,CCDS,ENSP,SWISSPROT,TREMBL,UNIPARC,UNIPROT_ISOFORM,RefSeq,MANE,APPRIS,FLAGS,SIFT,PolyPhen,EXON,INTRON,DOMAINS,1000G_AF,1000G_AFR_AF,1000G_AMR_AF,1000G_EAS_AF,1000G_EUR_AF,1000G_SAS_AF,ESP_AA_AF,ESP_EA_AF,gnomAD_AF,gnomAD_AFR_AF,gnomAD_AMR_AF,gnomAD_ASJ_AF,gnomAD_EAS_AF,gnomAD_FIN_AF,gnomAD_NFE_AF,gnomAD_OTH_AF,gnomAD_SAS_AF,MAX_AF,MAX_AF_POPS,gnomAD_non_cancer_AF,gnomAD_non_cancer_AFR_AF,gnomAD_non_cancer_AMI_AF,gnomAD_non_cancer_AMR_AF,gnomAD_non_cancer_ASJ_AF,gnomAD_non_cancer_EAS_AF,gnomAD_non_cancer_FIN_AF,gnomAD_non_cancer_MID_AF,gnomAD_non_cancer_NFE_AF,gnomAD_non_cancer_OTH_AF,gnomAD_non_cancer_SAS_AF,gnomAD_non_cancer_MAX_AF_adj,gnomAD_non_cancer_MAX_AF_POPS_adj,CLIN_SIG,SOMATIC,PUBMED,TRANSCRIPTION_FACTORS,MOTIF_NAME,MOTIF_POS,HIGH_INF_POS,MOTIF_SCORE_CHANGE,miRNA,IMPACT,PICK,VARIANT_CLASS,TSL,HGVS_OFFSET,PHENO,GENE_PHENO,CONTEXT,tumor_bam_uuid,normal_bam_uuid,case_id,GDC_FILTER,COSMIC,hotspot,RNA_Support,RNA_depth,RNA_ref_count,RNA_alt_count,callers
NEXN,91624,BI,GRCh38,chr1,77929416,77929416,+,Missense_Mutation,SNP,G,G,C,,,TCGA-CD-5802-01A-11D-1600-08,TCGA-CD-5802-10A-01D-1600-08,,,,,,,,,Somatic,,,,,,,c1b44966-0f72-4c4f-8783-ab3ffe7f17b2,af722e36-4912-45c4-b431-a2ceff596bac,c.965G>C,p.Arg322Thr,p.R322T,ENST00000334785,9/13,102,72,30,116,,,"NEXN,missense_variant,p.R322T,ENST00000334785,NM_144573.4,c.965G>C,MODERATE,YES,tolerated(0.17),benign(0.034),1;NEXN,missense_variant,p.R258T,ENST00000330010,NM_001172309.1,c.773G>C,MODERATE,,tolerated(0.1),benign(0.034),1;NEXN,missense_variant,p.R222T,ENST00000342754,,c.665G>C,MODERATE,,tolerated(0.13),benign(0.405),1;NEXN,missense_variant,p.R308T,ENST00000440324,,c.923G>C,MODERATE,,tolerated(0.3),benign(0.014),1;NEXN,missense_variant,p.R258T,ENST00000401035,,c.773G>C,MODERATE,,tolerated(0.19),benign(0.034),1;NEXN,upstream_gene_variant,,ENST00000480732,,,MODIFIER,,,,1;NEXN,non_coding_transcript_exon_variant,,ENST00000464998,,n.425G>C,MODIFIER,,,,1",C,ENSG00000162614,ENST00000334785,Transcript,missense_variant,missense_variant,1153/3282,965/2028,322/675,R/T,aGa/aCa,COSV57357195,,1,NEXN,HGNC,HGNC:29557,protein_coding,YES,CCDS41351.1,ENSP00000333938,Q0ZGT2.133,,UPI000022ABDC,Q0ZGT2-1,NM_144573.4,NM_144573.4,P3,,tolerated(0.17),benign(0.034),9/13,,Low_complexity_(Seg):seg;MobiDB_lite:mobidb-lite;Coiled-coils_(Ncoils):Coil;PANTHER:PTHR10075:SF52;PANTHER:PTHR10075,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1,,,,,,,,MODERATE,1.0,SNV,1.0,,1,1.0,AAGAAGAGAAG,7038f799-3e06-4998-b3c1-69f598faf0b4,836fb985-3ef2-4bd1-9e7c-092e897499f8,0aecac64-5982-4d76-8f31-958f6a00951d,,COSM4009978;COSM4009979,N,Unknown,,,,muse;mutect2;varscan2
COL24A1,255631,BI,GRCh38,chr1,86125858,86125858,+,Missense_Mutation,SNP,C,C,T,rs1320375371,,TCGA-CD-5802-01A-11D-1600-08,TCGA-CD-5802-10A-01D-1600-08,,,,,,,,,Somatic,,,,,,,c1b44966-0f72-4c4f-8783-ab3ffe7f17b2,af722e36-4912-45c4-b431-a2ceff596bac,c.478G>A,p.Asp160Asn,p.D160N,ENST00000370571,3/60,106,99,7,103,,,"COL24A1,missense_variant,p.D160N,ENST00000370571,NM_152890.7&NM_001349955.1,c.478G>A,MODERATE,YES,tolerated(0.27),benign(0.061),-1;COL24A1,downstream_gene_variant,,ENST00000496682,,,MODIFIER,,,,-1;COL24A1,missense_variant,p.D160N,ENST00000426639,,c.478G>A,MODERATE,,tolerated(0.42),benign(0.036),-1",T,ENSG00000171502,ENST00000370571,Transcript,missense_variant,missense_variant,854/6834,478/5145,160/1714,D/N,Gat/Aat,rs1320375371;COSV65305903,,-1,COL24A1,HGNC,HGNC:20821,protein_coding,YES,CCDS41353.1,ENSP00000359603,Q17RW2.126,,UPI000013E81F,Q17RW2-1,NM_152890.7;NM_001349955.1,NM_152890.7,P1,,tolerated(0.27),benign(0.061),3/60,,Gene3D:2.60.120.200;SMART:SM00210;Superfamily:SSF49899,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,0;1,,,,,,,,MODERATE,1.0,SNV,1.0,,0;1,,CTCATCATGAA,7038f799-3e06-4998-b3c1-69f598faf0b4,836fb985-3ef2-4bd1-9e7c-092e897499f8,0aecac64-5982-4d76-8f31-958f6a00951d,,COSM4010328,N,Unknown,,,,muse;mutect2
LRRC8B,23507,BI,GRCh38,chr1,89593023,89593023,+,Frame_Shift_Del,DEL,A,A,-,,,TCGA-CD-5802-01A-11D-1600-08,TCGA-CD-5802-10A-01D-1600-08,,,,,,,,,Somatic,,,,,,,c1b44966-0f72-4c4f-8783-ab3ffe7f17b2,af722e36-4912-45c4-b431-a2ceff596bac,c.2392del,p.Thr798ArgfsTer3,p.T798Rfs*3,ENST00000330947,6/6,222,176,46,246,,,"LRRC8B,frameshift_variant,p.T798Rfs*3,ENST00000640258,NM_015350.4&NM_001134476.2,c.2392del,HIGH,YES,,,1;LRRC8B,frameshift_variant,p.T798Rfs*3,ENST00000639264,,c.2392del,HIGH,,,,1;LRRC8B,frameshift_variant,p.T798Rfs*3,ENST00000330947,NM_001369819.2&NM_001369817.2,c.2392del,HIGH,,,,1;LRRC8B,3_prime_UTR_variant,,ENST00000439853,,c.*252del,MODIFIER,,,,1;LRRC8C-DT,intron_variant,,ENST00000443562,,n.403+2138del,MODIFIER,,,,-1;LRRC8C-DT,intron_variant,,ENST00000655657,,n.394-4938del,MODIFIER,,,,-1;LRRC8C-DT,intron_variant,,ENST00000666228,,n.219-4938del,MODIFIER,,,,-1;LRRC8C-DT,upstream_gene_variant,,ENST00000660444,,,MODIFIER,,,,-1",-,ENSG00000197147,ENST00000330947,Transcript,frameshift_variant,frameshift_variant,2826/7664,2392/2412,798/803,T/X,Acg/cg,COSV58376760,,1,LRRC8B,HGNC,HGNC:30692,protein_coding,,CCDS724.1,ENSP00000332674,Q6P9F7.148,A0A384N5V6.9,UPI00000739FF,,NM_001369819.2;NM_001369817.2,NM_001369817.2,P1,,,,6/6,,PANTHER:PTHR45752;PANTHER:PTHR45752:SF40;Gene3D:3.80.10.10,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1,,,,,,,,HIGH,,deletion,5.0,,1,,TTACAGACGTGC,7038f799-3e06-4998-b3c1-69f598faf0b4,836fb985-3ef2-4bd1-9e7c-092e897499f8,0aecac64-5982-4d76-8f31-958f6a00951d,,,N,Unknown,,,,mutect2;pindel;varscan2
BPNT1,10380,BI,GRCh38,chr1,220069429,220069429,+,Missense_Mutation,SNP,C,C,T,rs564542643,,TCGA-CD-5802-01A-11D-1600-08,TCGA-CD-5802-10A-01D-1600-08,,,,,,,,,Somatic,,,,,,,c1b44966-0f72-4c4f-8783-ab3ffe7f17b2,af722e36-4912-45c4-b431-a2ceff596bac,c.337G>A,p.Val113Met,p.V113M,ENST00000322067,5/9,134,105,29,130,,,"BPNT1,missense_variant,p.V113M,ENST00000469520,,c.337G>A,MODERATE,YES,deleterious(0),probably_damaging(0.978),-1;BPNT1,missense_variant,p.V113M,ENST00000322067,NM_006085.6,c.337G>A,MODERATE,,deleterious(0),probably_damaging(0.978),-1;BPNT1,missense_variant,p.V58M,ENST00000544404,NM_001286151.1&NM_001286149.2,c.172G>A,MODERATE,,deleterious(0),probably_damaging(0.978),-1;BPNT1,missense_variant,p.V77M,ENST00000414869,NM_001286150.1,c.229G>A,MODERATE,,deleterious(0),probably_damaging(0.967),-1;BPNT1,missense_variant,p.V113M,ENST00000354807,,c.337G>A,MODERATE,,deleterious(0),probably_damaging(0.993),-1;BPNT1,missense_variant,p.V77M,ENST00000463953,,c.229G>A,MODERATE,,deleterious(0),probably_damaging(0.967),-1;BPNT1,missense_variant,p.V58M,ENST00000480959,,c.172G>A,MODERATE,,deleterious(0),probably_damaging(0.978),-1;BPNT1,missense_variant,p.V113M,ENST00000498237,,c.337G>A,MODERATE,,deleterious(0),probably_damaging(0.978),-1;BPNT1,missense_variant,p.V77M,ENST00000498791,,c.229G>A,MODERATE,,deleterious(0),probably_damaging(0.967),-1;BPNT1,non_coding_transcript_exon_variant,,ENST00000482136,,n.157G>A,MODIFIER,,,,-1;BPNT1,non_coding_transcript_exon_variant,,ENST00000548668,,n.213G>A,MODIFIER,,,,-1",T,ENSG00000162813,ENST00000322067,Transcript,missense_variant,missense_variant,448/2400,337/927,113/308,V/M,Gtg/Atg,rs564542643;COSV59039886,,-1,BPNT1,HGNC,HGNC:1096,protein_coding,,CCDS41469.1,ENSP00000318852,O95861.167,V9HWF9.49,UPI000007212C,O95861-1,NM_006085.6,NM_006085.6,P1,,deleterious(0),probably_damaging(0.978),5/9,,PDB-ENSP_mappings:2wef.A;Gene3D:3.30.540.10;Pfam:PF00459;PANTHER:PTHR43028;PANTHER:PTHR43028:SF5;Superfamily:SSF56655;CDD:cd01640,0.0002,0.0,0.0014,0.0,0.0,0.0,,,1.676e-05,0.0,6.439e-05,0.0,0.0,0.0,9.058e-06,0.0,3.574e-05,0.0014,AMR,2.030150062637404e-05,0.0,0.0,0.0001325379998888,0.0,0.0,0.0,0.0,1.5435900422744453e-05,0.0,0.0,0.0001325379998888,amr,,0;1,,,,,,,,MODERATE,,SNV,1.0,,0;1,,GACCACGAGCT,7038f799-3e06-4998-b3c1-69f598faf0b4,836fb985-3ef2-4bd1-9e7c-092e897499f8,0aecac64-5982-4d76-8f31-958f6a00951d,,COSM4028374,N,Unknown,,,,muse;mutect2;varscan2
KCNF1,3754,BI,GRCh38,chr2,10913244,10913244,+,Missense_Mutation,SNP,C,C,T,,,TCGA-CD-5802-01A-11D-1600-08,TCGA-CD-5802-10A-01D-1600-08,,,,,,,,,Somatic,,,,,,,c1b44966-0f72-4c4f-8783-ab3ffe7f17b2,af722e36-4912-45c4-b431-a2ceff596bac,c.818C>T,p.Thr273Met,p.T273M,ENST00000295082,1/1,69,56,12,55,,,"KCNF1,missense_variant,p.T273M,ENST00000295082,NM_002236.5,c.818C>T,MODERATE,YES,deleterious(0),probably_damaging(0.997),1",T,ENSG00000162975,ENST00000295082,Transcript,missense_variant,missense_variant,1311/2292,818/1485,273/494,T/M,aCg/aTg,COSV54463336,,1,KCNF1,HGNC,HGNC:6246,protein_coding,YES,CCDS1676.1,ENSP00000295082,Q9H3M0.153,,UPI000012DC98,,NM_002236.5,NM_002236.5,P1,,deleterious(0),probably_damaging(0.997),1/1,,Gene3D:1.20.120.350;Pfam:PF00520;PANTHER:PTHR11537;PANTHER:PTHR11537:SF171;Superfamily:SSF81324,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1,,,,,,,,MODERATE,1.0,SNV,,,1,,GCTCACGCACC,7038f799-3e06-4998-b3c1-69f598faf0b4,836fb985-3ef2-4bd1-9e7c-092e897499f8,0aecac64-5982-4d76-8f31-958f6a00951d,,COSM4084154,N,Unknown,,,,muse;mutect2;varscan2
GDF7,151449,BI,GRCh38,chr2,20671299,20671299,+,Silent,SNP,G,G,A,rs1182817522,,TCGA-CD-5802-01A-11D-1600-08,TCGA-CD-5802-10A-01D-1600-08,,,,,,,,,Somatic,,,,,,,c1b44966-0f72-4c4f-8783-ab3ffe7f17b2,af722e36-4912-45c4-b431-a2ceff596bac,c.1227G>A,p.Ala409=,p.A409=,ENST00000272224,2/2,36,29,7,36,,,"GDF7,synonymous_variant,p.A409=,ENST00000272224,NM_182828.4,c.1227G>A,LOW,YES,,,1",A,ENSG00000143869,ENST00000272224,Transcript,synonymous_variant,synonymous_variant,1323/9267,1227/1353,409/450,A,gcG/gcA,rs1182817522;COSV55347665,,1,GDF7,HGNC,HGNC:4222,protein_coding,YES,CCDS1701.1,ENSP00000272224,Q7Z4P5.116,,UPI0000208B29,,NM_182828.4,NM_182828.4,P1,,,,2/2,,Gene3D:2.10.90.10;Pfam:PF00019;PROSITE_profiles:PS51362;PANTHER:PTHR11848;PANTHER:PTHR11848:SF160;SMART:SM00204;Superfamily:SSF57501,,,,,,,,,,,,,,,,,,,,6.759220013918821e-06,0.0,0.0,0.0,0.0,0.0,0.0,0.0,1.543160033179447e-05,0.0,0.0,,,,0;1,,,,,,,,LOW,1.0,SNV,1.0,,0;1,,GACGCGGCGCC,7038f799-3e06-4998-b3c1-69f598faf0b4,836fb985-3ef2-4bd1-9e7c-092e897499f8,0aecac64-5982-4d76-8f31-958f6a00951d,,COSM4090652,N,Unknown,,,,muse;mutect2
TCF23,150921,BI,GRCh38,chr2,27150326,27150326,+,Silent,SNP,G,G,A,rs1044613600,,TCGA-CD-5802-01A-11D-1600-08,TCGA-CD-5802-10A-01D-1600-08,,,,,,,,,Somatic,,,,,,,c1b44966-0f72-4c4f-8783-ab3ffe7f17b2,af722e36-4912-45c4-b431-a2ceff596bac,c.426G>A,p.Pro142=,p.P142=,ENST00000296096,2/3,381,313,67,378,,,"TCF23,synonymous_variant,p.P142=,ENST00000296096,NM_175769.3,c.426G>A,LOW,YES,,,1;TCF23,downstream_gene_variant,,ENST00000407815,,,MODIFIER,,,,1",A,ENSG00000163792,ENST00000296096,Transcript,synonymous_variant,synonymous_variant,556/4882,426/645,142/214,P,ccG/ccA,rs1044613600;COSV56077846;COSV56078859,,1,TCF23,HGNC,HGNC:18602,protein_coding,YES,CCDS33163.1,ENSP00000296096,Q7RTU1.116,,UPI00001AEC06,,NM_175769.3,NM_175769.3,P1,,,,2/3,,PANTHER:PTHR23349:SF58;PANTHER:PTHR23349,,,,,,,,,8.016e-06,0.0,0.0,0.0,0.0,0.0,8.886e-06,0.0,3.279e-05,3.279e-05,gnomAD_SAS,1.3518400010070764e-05,2.430960012134165e-05,0.0,6.62339007249102e-05,0.0,0.0,0.0,0.0,0.0,0.0,0.0,,,,0;1;1,,,,,,,,LOW,1.0,SNV,1.0,,0;1;1,,TGGCCGCCCTT,7038f799-3e06-4998-b3c1-69f598faf0b4,836fb985-3ef2-4bd1-9e7c-092e897499f8,0aecac64-5982-4d76-8f31-958f6a00951d,,COSM4093477,N,Unknown,,,,muse;mutect2;varscan2
GPR39,2863,BI,GRCh38,chr2,132417721,132417721,+,Missense_Mutation,SNP,G,G,A,,,TCGA-CD-5802-01A-11D-1600-08,TCGA-CD-5802-10A-01D-1600-08,,,,,,,,,Somatic,,,,,,,c1b44966-0f72-4c4f-8783-ab3ffe7f17b2,af722e36-4912-45c4-b431-a2ceff596bac,c.679G>A,p.Ala227Thr,p.A227T,ENST00000329321,1/2,79,61,18,100,,,"GPR39,missense_variant,p.A227T,ENST00000329321,NM_001508.3,c.679G>A,MODERATE,YES,deleterious(0.01),probably_damaging(0.979),1;GPR39,missense_variant,p.A227T,ENST00000622084,,c.679G>A,MODERATE,,deleterious(0),probably_damaging(0.99),1",A,ENSG00000183840,ENST00000329321,Transcript,missense_variant,missense_variant,917/2576,679/1362,227/453,A/T,Gcc/Acc,COSV61423325,,1,GPR39,HGNC,HGNC:4496,protein_coding,YES,CCDS2170.1,ENSP00000327417,O43194.159,,UPI0000046406,,NM_001508.3,NM_001508.3,P1,,deleterious(0.01),probably_damaging(0.979),1/2,,Superfamily:SSF81321;Gene3D:1.20.1070.10;Pfam:PF00001;PANTHER:PTHR46752;CDD:cd15135;PROSITE_profiles:PS50262;Transmembrane_helices:TMhelix,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1,,,,,,,,MODERATE,1.0,SNV,1.0,,1,,TCGGCGCCTTC,7038f799-3e06-4998-b3c1-69f598faf0b4,836fb985-3ef2-4bd1-9e7c-092e897499f8,0aecac64-5982-4d76-8f31-958f6a00951d,,COSM4084902,N,Unknown,,,,muse;mutect2;varscan2
ZC3H15,55854,BI,GRCh38,chr2,186504205,186504206,+,Frame_Shift_Ins,INS,-,-,GA,novel,,TCGA-CD-5802-01A-11D-1600-08,TCGA-CD-5802-10A-01D-1600-08,,,,,,,,,Somatic,,,,,,,c1b44966-0f72-4c4f-8783-ab3ffe7f17b2,af722e36-4912-45c4-b431-a2ceff596bac,c.716_717dup,p.Arg240SerfsTer5,p.R240Sfs*5,ENST00000337859,6/10,124,102,22,98,,,"ZC3H15,frameshift_variant,p.R240Sfs*5,ENST00000337859,NM_018471.3,c.716_717dup,HIGH,YES,,,1;ZC3H15,upstream_gene_variant,,ENST00000445547,,,MODIFIER,,,,1;ZC3H15,downstream_gene_variant,,ENST00000468120,,,MODIFIER,,,,1;ZC3H15,downstream_gene_variant,,ENST00000481101,,,MODIFIER,,,,1;ZC3H15,downstream_gene_variant,,ENST00000496289,,,MODIFIER,,,,1;ZC3H15,3_prime_UTR_variant,,ENST00000421536,,c.*153_*154dup,MODIFIER,,,,1;ZC3H15,downstream_gene_variant,,ENST00000437396,,,MODIFIER,,,,1;ZC3H15,upstream_gene_variant,,ENST00000498757,,,MODIFIER,,,,1",GA,ENSG00000065548,ENST00000337859,Transcript,frameshift_variant,frameshift_variant,831-832/2032,708-709/1281,236-237/426,-/X,-/GA,,,1,ZC3H15,HGNC,HGNC:29528,protein_coding,YES,CCDS42791.1,ENSP00000338788,Q8WU90.147,,UPI00000437CE,Q8WU90-1,NM_018471.3,NM_018471.3,P1,,,,6/10,,Pfam:PF16543;PANTHER:PTHR12681;PANTHER:PTHR12681:SF0;Low_complexity_(Seg):seg,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,HIGH,1.0,insertion,1.0,9.0,,,CTAATTGAGAG,7038f799-3e06-4998-b3c1-69f598faf0b4,836fb985-3ef2-4bd1-9e7c-092e897499f8,0aecac64-5982-4d76-8f31-958f6a00951d,,,N,Unknown,,,,mutect2;varscan2
TNS1,7145,BI,GRCh38,chr2,217818710,217818710,+,Missense_Mutation,SNP,G,G,A,rs373946458,,TCGA-CD-5802-01A-11D-1600-08,TCGA-CD-5802-10A-01D-1600-08,,,,,,,,,Somatic,,,,,,,c1b44966-0f72-4c4f-8783-ab3ffe7f17b2,af722e36-4912-45c4-b431-a2ceff596bac,c.3310C>T,p.Arg1104Trp,p.R1104W,ENST00000171887,24/33,68,56,12,98,,,"TNS1,missense_variant,p.R1229W,ENST00000646520,,c.3685C>T,MODERATE,YES,tolerated(0.1),benign(0),-1;TNS1,missense_variant,p.R1104W,ENST00000171887,NM_022648.6,c.3310C>T,MODERATE,,deleterious(0.04),benign(0),-1;TNS1,missense_variant,p.R1196W,ENST00000651849,,c.3586C>T,MODERATE,,deleterious(0.05),benign(0.04),-1;TNS1,missense_variant,p.R1091W,ENST00000611415,,c.3271C>T,MODERATE,,tolerated(0.07),benign(0),-1;TNS1,missense_variant,p.R734W,ENST00000615025,,c.2200C>T,MODERATE,,tolerated(0.15),benign(0),-1;TNS1,missense_variant,p.R1091W,ENST00000419504,NM_001308022.1,c.3271C>T,MODERATE,,tolerated(0.07),benign(0),-1;TNS1,missense_variant,p.R1083W,ENST00000430930,NM_001308023.2,c.3247C>T,MODERATE,,tolerated(0.1),benign(0),-1;TNS1,missense_variant,p.R215W,ENST00000446688,,c.643C>T,MODERATE,,tolerated(0.2),benign(0),-1;TNS1,upstream_gene_variant,,ENST00000490566,,,MODIFIER,,,,-1;TNS1,upstream_gene_variant,,ENST00000495556,,,MODIFIER,,,,-1",A,ENSG00000079308,ENST00000171887,Transcript,missense_variant,missense_variant,3763/10331,3310/5208,1104/1735,R/W,Cgg/Tgg,rs373946458;COSV50702187,,-1,TNS1,HGNC,HGNC:11973,protein_coding,,CCDS2407.1,ENSP00000171887,Q9HBL0.168,,UPI0000456EEB,Q9HBL0-1,NM_022648.6,,,,deleterious(0.04),benign(0),24/33,,PANTHER:PTHR45734;PANTHER:PTHR45734:SF3;MobiDB_lite:mobidb-lite,,,,,,,,,8.036e-06,0.0,0.0,0.0,0.0,0.0,1.784e-05,0.0,0.0,1.784e-05,gnomAD_NFE,6.759500138286967e-06,0.0,0.0,0.0,0.0,0.0,0.0,0.0,1.543160033179447e-05,0.0,0.0,,,,0;1,,,,,,,,MODERATE,,SNV,1.0,,0;1,,CGTCCGGGGAC,7038f799-3e06-4998-b3c1-69f598faf0b4,836fb985-3ef2-4bd1-9e7c-092e897499f8,0aecac64-5982-4d76-8f31-958f6a00951d,,COSM4091355,N,Unknown,,,,muse;mutect2
KCNH8,131096,BI,GRCh38,chr3,19342715,19342715,+,Splice_Site,SNP,G,G,A,rs755303397,,TCGA-CD-5802-01A-11D-1600-08,TCGA-CD-5802-10A-01D-1600-08,,,,,,,,,Somatic,,,,,,,c1b44966-0f72-4c4f-8783-ab3ffe7f17b2,af722e36-4912-45c4-b431-a2ceff596bac,c.570+1G>A,,p.X190_splice,ENST00000328405,,133,105,27,176,,,"KCNH8,splice_donor_variant,p.X190_splice,ENST00000328405,NM_144633.3,c.570+1G>A,HIGH,YES,,,1;KCNH8,splice_donor_variant,p.X190_splice,ENST00000452398,,c.570+1G>A,HIGH,,,,1",A,ENSG00000183960,ENST00000328405,Transcript,splice_donor_variant,splice_donor_variant,,,,,,rs755303397;COSV60463215,,1,KCNH8,HGNC,HGNC:18864,protein_coding,YES,CCDS2632.1,ENSP00000328813,Q96L42.167,,UPI0000167D12,Q96L42-1,NM_144633.3,NM_144633.3,P1,,,,,4/15,,,,,,,,,,1.201e-05,0.0,2.913e-05,0.0,0.0,0.0,8.862e-06,0.0,3.274e-05,3.274e-05,gnomAD_SAS,6.764889803889673e-06,0.0,0.0,0.0,0.000303030014038,0.0,0.0,0.0,0.0,0.0,0.0,,,,0;1,,,,,,,,HIGH,1.0,SNV,1.0,,0;1,,ATAACGTAGGT,7038f799-3e06-4998-b3c1-69f598faf0b4,836fb985-3ef2-4bd1-9e7c-092e897499f8,0aecac64-5982-4d76-8f31-958f6a00951d,NonExonic,COSM4116137,N,Unknown,,,,muse;mutect2;varscan2
FOXL2NB,401089,BI,GRCh38,chr3,138950445,138950445,+,Missense_Mutation,SNP,G,G,C,rs757845000,,TCGA-CD-5802-01A-11D-1600-08,TCGA-CD-5802-10A-01D-1600-08,,,,,,,,,Somatic,,,,,,,c1b44966-0f72-4c4f-8783-ab3ffe7f17b2,af722e36-4912-45c4-b431-a2ceff596bac,c.401G>C,p.Gly134Ala,p.G134A,ENST00000383165,3/3,57,47,10,61,,,"FOXL2NB,missense_variant,p.G134A,ENST00000383165,NM_001040061.3,c.401G>C,MODERATE,YES,deleterious_low_confidence(0),benign(0.389),1;FOXL2,upstream_gene_variant,,ENST00000648323,NM_023067.4,,MODIFIER,YES,,,-1;FOXL2NB,3_prime_UTR_variant,,ENST00000470680,,c.*283G>C,MODIFIER,,,,1;FOXL2NB,non_coding_transcript_exon_variant,,ENST00000498709,,n.1330G>C,MODIFIER,,,,1",C,ENSG00000206262,ENST00000383165,Transcript,missense_variant,missense_variant,549/4094,401/528,134/175,G/A,gGa/gCa,rs757845000;COSV57727003,,1,FOXL2NB,HGNC,HGNC:34428,protein_coding,YES,CCDS43155.1,ENSP00000372651,Q6ZUU3.83,,UPI00001C0AE3,,NM_001040061.3,NM_001040061.3,P1,,deleterious_low_confidence(0),benign(0.389),3/3,,,,,,,,,,,4.02e-06,0.0,0.0,0.0,0.0,0.0,0.0,0.0,3.268e-05,3.268e-05,gnomAD_SAS,,,,,,,,,,,,,,,0;1,,,,,,,,MODERATE,1.0,SNV,2.0,,0;1,,AGCGGGACCCC,7038f799-3e06-4998-b3c1-69f598faf0b4,836fb985-3ef2-4bd1-9e7c-092e897499f8,0aecac64-5982-4d76-8f31-958f6a00951d,,COSM4113965,N,Unknown,,,,muse;mutect2;varscan2
GHSR,2693,BI,GRCh38,chr3,172447879,172447879,+,Missense_Mutation,SNP,A,A,T,,,TCGA-CD-5802-01A-11D-1600-08,TCGA-CD-5802-10A-01D-1600-08,,,,,,,,,Somatic,,,,,,,c1b44966-0f72-4c4f-8783-ab3ffe7f17b2,af722e36-4912-45c4-b431-a2ceff596bac,c.535T>A,p.Phe179Ile,p.F179I,ENST00000241256,1/2,48,43,5,71,,,"GHSR,missense_variant,p.F179I,ENST00000241256,NM_198407.2,c.535T>A,MODERATE,YES,deleterious(0.03),possibly_damaging(0.908),-1;GHSR,missense_variant,p.F179I,ENST00000427970,NM_004122.2,c.535T>A,MODERATE,,deleterious(0.03),probably_damaging(0.999),-1",T,ENSG00000121853,ENST00000241256,Transcript,missense_variant,missense_variant,578/3014,535/1101,179/366,F/I,Ttc/Atc,COSV53839193,,-1,GHSR,HGNC,HGNC:4267,protein_coding,YES,CCDS3218.1,ENSP00000241256,Q92847.178,,UPI000003C2FA,Q92847-1,NM_198407.2,NM_198407.2,P1,,deleterious(0.03),possibly_damaging(0.908),1/2,,Transmembrane_helices:TMhelix;PROSITE_profiles:PS50262;CDD:cd15131;PANTHER:PTHR24243;PANTHER:PTHR24243:SF7;Gene3D:1.20.1070.10;Pfam:PF00001;Superfamily:SSF81321;Prints:PR00237,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1,,,,,,,,MODERATE,1.0,SNV,1.0,,1,1.0,CACGAAGATGG,7038f799-3e06-4998-b3c1-69f598faf0b4,836fb985-3ef2-4bd1-9e7c-092e897499f8,0aecac64-5982-4d76-8f31-958f6a00951d,,COSM4115274;COSM4115275,N,Unknown,,,,muse;mutect2;varscan2
TBCCD1,55171,BI,GRCh38,chr3,186554399,186554401,+,In_Frame_Del,DEL,AGA,AGA,-,novel,,TCGA-CD-5802-01A-11D-1600-08,TCGA-CD-5802-10A-01D-1600-08,,,,,,,,,Somatic,,,,,,,c1b44966-0f72-4c4f-8783-ab3ffe7f17b2,af722e36-4912-45c4-b431-a2ceff596bac,c.1397_1399del,p.Phe466del,p.F466del,ENST00000338733,6/8,259,213,46,222,,,"TBCCD1,inframe_deletion,p.F466del,ENST00000424280,NM_001134415.1,c.1397_1399del,MODERATE,YES,,,-1;TBCCD1,inframe_deletion,p.F466del,ENST00000338733,NM_018138.5,c.1397_1399del,MODERATE,,,,-1;TBCCD1,inframe_deletion,p.F370del,ENST00000446782,NM_001286749.2,c.1109_1111del,MODERATE,,,,-1;TBCCD1,downstream_gene_variant,,ENST00000413695,,,MODIFIER,,,,-1;TBCCD1,downstream_gene_variant,,ENST00000430560,,,MODIFIER,,,,-1;TBCCD1,non_coding_transcript_exon_variant,,ENST00000479590,,n.75_77del,MODIFIER,,,,-1",-,ENSG00000113838,ENST00000338733,Transcript,inframe_deletion,inframe_deletion,1513-1515/2700,1397-1399/1674,466-467/557,FY/Y,tTCTat/tat,,,-1,TBCCD1,HGNC,HGNC:25546,protein_coding,,CCDS3276.1,ENSP00000341652,Q9NVR7.146,,UPI0000073055,Q9NVR7-1,NM_018138.5,NM_018138.5,P1,,,,6/8,,PANTHER:PTHR16052;PANTHER:PTHR16052:SF0;Gene3D:2.160.20.70,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,MODERATE,,deletion,1.0,,,,ATACATAGAATTCA,7038f799-3e06-4998-b3c1-69f598faf0b4,836fb985-3ef2-4bd1-9e7c-092e897499f8,0aecac64-5982-4d76-8f31-958f6a00951d,,,N,Unknown,,,,mutect2;pindel;varscan2
TBCCD1,55171,BI,GRCh38,chr3,186554557,186554557,+,Missense_Mutation,SNP,A,A,G,,,TCGA-CD-5802-01A-11D-1600-08,TCGA-CD-5802-10A-01D-1600-08,,,,,,,,,Somatic,,,,,,,c1b44966-0f72-4c4f-8783-ab3ffe7f17b2,af722e36-4912-45c4-b431-a2ceff596bac,c.1241T>C,p.Val414Ala,p.V414A,ENST00000338733,6/8,74,60,14,103,,,"TBCCD1,missense_variant,p.V414A,ENST00000424280,NM_001134415.1,c.1241T>C,MODERATE,YES,deleterious(0.02),benign(0.019),-1;TBCCD1,missense_variant,p.V414A,ENST00000338733,NM_018138.5,c.1241T>C,MODERATE,,deleterious(0.02),benign(0.019),-1;TBCCD1,missense_variant,p.V318A,ENST00000446782,NM_001286749.2,c.953T>C,MODERATE,,deleterious(0.02),benign(0.011),-1;TBCCD1,downstream_gene_variant,,ENST00000413695,,,MODIFIER,,,,-1;TBCCD1,downstream_gene_variant,,ENST00000430560,,,MODIFIER,,,,-1;TBCCD1,upstream_gene_variant,,ENST00000479590,,,MODIFIER,,,,-1",G,ENSG00000113838,ENST00000338733,Transcript,missense_variant,missense_variant,1357/2700,1241/1674,414/557,V/A,gTa/gCa,COSV58662111,,-1,TBCCD1,HGNC,HGNC:25546,protein_coding,,CCDS3276.1,ENSP00000341652,Q9NVR7.146,,UPI0000073055,Q9NVR7-1,NM_018138.5,NM_018138.5,P1,,deleterious(0.02),benign(0.019),6/8,,PROSITE_profiles:PS51329;PANTHER:PTHR16052;PANTHER:PTHR16052:SF0;Pfam:PF07986;Gene3D:2.160.20.70,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1,,,,,,,,MODERATE,,SNV,1.0,,1,,AAGTTACTGTC,7038f799-3e06-4998-b3c1-69f598faf0b4,836fb985-3ef2-4bd1-9e7c-092e897499f8,0aecac64-5982-4d76-8f31-958f6a00951d,,COSM4115934,N,Unknown,,,,muse;mutect2;varscan2
RFC4,5984,BI,GRCh38,chr3,186791832,186791832,+,Missense_Mutation,SNP,T,T,C,,,TCGA-CD-5802-01A-11D-1600-08,TCGA-CD-5802-10A-01D-1600-08,,,,,,,,,Somatic,,,,,,,c1b44966-0f72-4c4f-8783-ab3ffe7f17b2,af722e36-4912-45c4-b431-a2ceff596bac,c.694A>G,p.Lys232Glu,p.K232E,ENST00000296273,8/11,208,198,10,225,,,"RFC4,missense_variant,p.K232E,ENST00000392481,NM_181573.2,c.694A>G,MODERATE,YES,tolerated(0.69),benign(0),-1;RFC4,missense_variant,p.K232E,ENST00000296273,NM_002916.4,c.694A>G,MODERATE,,tolerated(0.69),benign(0),-1;RFC4,missense_variant,p.K232E,ENST00000433496,,c.694A>G,MODERATE,,tolerated(0.69),benign(0),-1;RFC4,missense_variant,p.K7E,ENST00000417876,,c.19A>G,MODERATE,,tolerated(0.94),benign(0.007),-1;EIF4A2,downstream_gene_variant,,ENST00000323963,NM_001967.4,,MODIFIER,,,,1;RFC4,downstream_gene_variant,,ENST00000418288,,,MODIFIER,,,,-1;RFC4,downstream_gene_variant,,ENST00000427785,,,MODIFIER,,,,-1;EIF4A2,downstream_gene_variant,,ENST00000440191,,,MODIFIER,YES,,,1;SNORA63,downstream_gene_variant,,ENST00000363450,,,MODIFIER,YES,,,1;SNORA81,downstream_gene_variant,,ENST00000408493,,,MODIFIER,YES,,,1;SNORA4,downstream_gene_variant,,ENST00000584302,,,MODIFIER,YES,,,1;RFC4,non_coding_transcript_exon_variant,,ENST00000494047,,n.884A>G,MODIFIER,,,,-1;RFC4,non_coding_transcript_exon_variant,,ENST00000479307,,n.421A>G,MODIFIER,,,,-1;RFC4,non_coding_transcript_exon_variant,,ENST00000460408,,n.486A>G,MODIFIER,,,,-1;EIF4A2,downstream_gene_variant,,ENST00000425053,,,MODIFIER,,,,1;EIF4A2,downstream_gene_variant,,ENST00000426808,,,MODIFIER,,,,1;EIF4A2,downstream_gene_variant,,ENST00000429589,,,MODIFIER,,,,1;EIF4A2,downstream_gene_variant,,ENST00000443963,,,MODIFIER,,,,1;RFC4,downstream_gene_variant,,ENST00000449502,,,MODIFIER,,,,-1;EIF4A2,downstream_gene_variant,,ENST00000461021,,,MODIFIER,,,,1;EIF4A2,downstream_gene_variant,,ENST00000465792,,,MODIFIER,,,,1;EIF4A2,downstream_gene_variant,,ENST00000468362,,,MODIFIER,,,,1;EIF4A2,downstream_gene_variant,,ENST00000475409,,,MODIFIER,,,,1;EIF4A2,downstream_gene_variant,,ENST00000475653,,,MODIFIER,,,,1;EIF4A2,downstream_gene_variant,,ENST00000485101,,,MODIFIER,,,,1;RFC4,downstream_gene_variant,,ENST00000489028,,,MODIFIER,,,,-1;EIF4A2,downstream_gene_variant,,ENST00000492144,,,MODIFIER,,,,1;EIF4A2,downstream_gene_variant,,ENST00000494445,,,MODIFIER,,,,1;EIF4A2,downstream_gene_variant,,ENST00000496382,,,MODIFIER,,,,1;EIF4A2,downstream_gene_variant,,ENST00000497177,,,MODIFIER,,,,1",C,ENSG00000163918,ENST00000296273,Transcript,missense_variant,missense_variant,917/1384,694/1092,232/363,K/E,Aaa/Gaa,COSV56216896,,-1,RFC4,HGNC,HGNC:9972,protein_coding,,CCDS3283.1,ENSP00000296273,P35249.202,,UPI0000125167,P35249-1,NM_002916.4,,P1,,tolerated(0.69),benign(0),8/11,,PDB-ENSP_mappings:6vvo.D;CDD:cd18140;PANTHER:PTHR11669:SF20;PANTHER:PTHR11669;Gene3D:1.10.8.60;Superfamily:SSF52540,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1,,,,,,,,MODERATE,,SNV,1.0,,1,,CACTTTAACAA,7038f799-3e06-4998-b3c1-69f598faf0b4,836fb985-3ef2-4bd1-9e7c-092e897499f8,0aecac64-5982-4d76-8f31-958f6a00951d,,COSM4115973,N,Unknown,,,,muse;mutect2
C4orf50,389197,BI,GRCh38,chr4,5967444,5967444,+,Missense_Mutation,SNP,C,C,T,rs750915133,,TCGA-CD-5802-01A-11D-1600-08,TCGA-CD-5802-10A-01D-1600-08,,,,,,,,,Somatic,,,,,,,c1b44966-0f72-4c4f-8783-ab3ffe7f17b2,af722e36-4912-45c4-b431-a2ceff596bac,c.427G>A,p.Val143Ile,p.V143I,ENST00000324058,5/8,93,66,27,185,,,"C4orf50,missense_variant,p.V1375I,ENST00000531445,NM_001364690.1&NM_001364689.1,c.4123G>A,MODERATE,YES,tolerated(0.19),benign(0.007),-1;C4orf50,missense_variant,p.V143I,ENST00000324058,,c.427G>A,MODERATE,,tolerated(0.16),benign(0.001),-1;C4orf50,missense_variant,p.V715I,ENST00000639345,,c.2143G>A,MODERATE,,tolerated(0.21),benign(0.007),-1",T,ENSG00000181215,ENST00000324058,Transcript,missense_variant,missense_variant,1725/5201,427/831,143/276,V/I,Gtc/Atc,rs750915133;COSV100135761;COSV60688547,,-1,C4orf50,HGNC,HGNC:33766,protein_coding,,,ENSP00000317287,Q6ZRC1.90,,UPI00001C0FBD,,,,A2,,tolerated(0.16),benign(0.001),5/8,,Pfam:PF15030;PANTHER:PTHR36866,,,,,,,,,1.591e-05,0.0,0.0,0.0,0.0,4.624e-05,2.637e-05,0.0,0.0,4.624e-05,gnomAD_FIN,2.0276000213925727e-05,0.0,0.0,0.0,0.0,0.0,0.0,0.0,4.628629903891124e-05,0.0,0.0,4.628629903891124e-05,nfe,,0;1;1,,,,,,,,MODERATE,,SNV,2.0,,0;1;1,,CTTGACGTCCA,7038f799-3e06-4998-b3c1-69f598faf0b4,836fb985-3ef2-4bd1-9e7c-092e897499f8,0aecac64-5982-4d76-8f31-958f6a00951d,,COSM4125359;COSM4125360,N,Unknown,,,,muse;mutect2;varscan2
ASB5,140458,BI,GRCh38,chr4,176221236,176221236,+,Nonsense_Mutation,SNP,C,C,A,,,TCGA-CD-5802-01A-11D-1600-08,TCGA-CD-5802-10A-01D-1600-08,,,,,,,,,Somatic,,,,,,,c1b44966-0f72-4c4f-8783-ab3ffe7f17b2,af722e36-4912-45c4-b431-a2ceff596bac,c.589G>T,p.Glu197Ter,p.E197*,ENST00000296525,5/7,110,98,12,112,,,"ASB5,stop_gained,p.E197*,ENST00000296525,NM_080874.4,c.589G>T,HIGH,YES,,,-1;ASB5,stop_gained,p.E152*,ENST00000672074,,c.454G>T,HIGH,,,,-1;ASB5,stop_gained,p.E144*,ENST00000512254,,c.430G>T,HIGH,,,,-1;ASB5,downstream_gene_variant,,ENST00000510578,,,MODIFIER,,,,-1;ASB5,downstream_gene_variant,,ENST00000511879,,,MODIFIER,,,,-1",A,ENSG00000164122,ENST00000296525,Transcript,stop_gained,stop_gained,703/3031,589/990,197/329,E/*,Gaa/Taa,COSV56668461;COSV56670474,,-1,ASB5,HGNC,HGNC:17180,protein_coding,YES,CCDS3827.1,ENSP00000296525,Q8WWX0.150,Q5HYF3.146,UPI00000015CF,Q8WWX0-1,NM_080874.4,NM_080874.4,P1,,,,5/7,,PROSITE_profiles:PS50297;PANTHER:PTHR24136:SF18;PANTHER:PTHR24136;Gene3D:1.25.40.20;Pfam:PF12796;Superfamily:SSF48403,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1;1,,,,,,,,HIGH,1.0,SNV,1.0,,1;1,,AATTTCTTGGT,7038f799-3e06-4998-b3c1-69f598faf0b4,836fb985-3ef2-4bd1-9e7c-092e897499f8,0aecac64-5982-4d76-8f31-958f6a00951d,,COSM1053427,N,Unknown,,,,muse;mutect2
F12,2161,BI,GRCh38,chr5,177405123,177405123,+,Missense_Mutation,SNP,C,C,T,,,TCGA-CD-5802-01A-11D-1600-08,TCGA-CD-5802-10A-01D-1600-08,,,,,,,,,Somatic,,,,,,,c1b44966-0f72-4c4f-8783-ab3ffe7f17b2,af722e36-4912-45c4-b431-a2ceff596bac,c.460G>A,p.Glu154Lys,p.E154K,ENST00000253496,6/14,110,86,23,160,,,"F12,missense_variant,p.E154K,ENST00000253496,NM_000505.4,c.460G>A,MODERATE,YES,tolerated(0.57),possibly_damaging(0.519),-1;GRK6,intron_variant,,ENST00000502598,,c.-45+1597C>T,MODIFIER,,,,1;GRK6,intron_variant,,ENST00000506296,,c.-45+566C>T,MODIFIER,,,,1;PFN3,upstream_gene_variant,,ENST00000358571,NM_001029886.3,,MODIFIER,YES,,,-1;F12,upstream_gene_variant,,ENST00000514943,,,MODIFIER,,,,-1;F12,upstream_gene_variant,,ENST00000502854,,,MODIFIER,,,,-1;F12,upstream_gene_variant,,ENST00000503736,,,MODIFIER,,,,-1;F12,upstream_gene_variant,,ENST00000504406,,,MODIFIER,,,,-1;F12,upstream_gene_variant,,ENST00000510358,,,MODIFIER,,,,-1",T,ENSG00000131187,ENST00000253496,Transcript,missense_variant,missense_variant,497/2036,460/1848,154/615,E/K,Gag/Aag,COSV53691320,,-1,F12,HGNC,HGNC:3530,protein_coding,YES,CCDS34302.1,ENSP00000253496,P00748.232,,UPI000048055F,,NM_000505.4,NM_000505.4,P1,,tolerated(0.57),possibly_damaging(0.519),6/14,,PDB-ENSP_mappings:4bdw.A;PDB-ENSP_mappings:4bdx.A;CDD:cd00061;Pfam:PF00039;Gene3D:2.10.25.10;PIRSF:PIRSF001146;SMART:SM00058;PROSITE_profiles:PS51091;PANTHER:PTHR24264;PANTHER:PTHR24264:SF46;PROSITE_patterns:PS01253,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1,,,,,,,,MODERATE,1.0,SNV,1.0,,1,1.0,TTGCTCAGTTC,7038f799-3e06-4998-b3c1-69f598faf0b4,836fb985-3ef2-4bd1-9e7c-092e897499f8,0aecac64-5982-4d76-8f31-958f6a00951d,,COSM3854010,N,Unknown,,,,muse;mutect2;varscan2
ZFP57,346171,BI,GRCh38,chr6,29676051,29676051,+,Silent,SNP,G,G,A,,,TCGA-CD-5802-01A-11D-1600-08,TCGA-CD-5802-10A-01D-1600-08,,,,,,,,,Somatic,,,,,,,c1b44966-0f72-4c4f-8783-ab3ffe7f17b2,af722e36-4912-45c4-b431-a2ceff596bac,c.132C>T,p.Val44=,p.V44=,ENST00000376883,3/5,260,192,68,392,,,"ZFP57,synonymous_variant,p.V44=,ENST00000376883,NM_001109809.5,c.132C>T,LOW,YES,,,-1;ZFP57,5_prime_UTR_variant,,ENST00000488757,NM_001366333.2,c.-85C>T,MODIFIER,,,,-1;MOG,downstream_gene_variant,,ENST00000376888,NM_206814.6,,MODIFIER,,,,1;MOG,downstream_gene_variant,,ENST00000376891,NM_001008229.3,,MODIFIER,,,,1;MOG,downstream_gene_variant,,ENST00000376894,NM_001363610.2,,MODIFIER,YES,,,1;MOG,downstream_gene_variant,,ENST00000376898,NM_002433.5,,MODIFIER,,,,1;MOG,downstream_gene_variant,,ENST00000376917,NM_206809.4,,MODIFIER,,,,1;MOG,downstream_gene_variant,,ENST00000396701,NM_206810.4,,MODIFIER,,,,1;MOG,downstream_gene_variant,,ENST00000396704,NM_001008228.3,,MODIFIER,,,,1;MOG,downstream_gene_variant,,ENST00000416766,,,MODIFIER,,,,1;MOG,downstream_gene_variant,,ENST00000431798,NM_206812.4,,MODIFIER,,,,1;MOG,downstream_gene_variant,,ENST00000483013,,,MODIFIER,,,,1;MOG,downstream_gene_variant,,ENST00000490427,NM_001170418.2,,MODIFIER,,,,1;MOG,downstream_gene_variant,,ENST00000494692,NM_206811.4,,MODIFIER,,,,1;MOG,downstream_gene_variant,,ENST00000376889,,,MODIFIER,,,,1;MOG,downstream_gene_variant,,ENST00000485211,,,MODIFIER,,,,1",A,ENSG00000204644,ENST00000376883,Transcript,synonymous_variant,synonymous_variant,586/2082,132/1611,44/536,V,gtC/gtT,COSV65306088,,-1,ZFP57,HGNC,HGNC:18791,protein_coding,YES,CCDS43436.2,ENSP00000366080,Q9NU63.152,A0A1U9X8V5.21,UPI0001951170,Q9NU63-2,NM_001109809.5,NM_001109809.5,P1,,,,3/5,,Pfam:PF01352;PROSITE_profiles:PS50805;PANTHER:PTHR24381;PANTHER:PTHR24381:SF277;SMART:SM00349;Superfamily:SSF109640;CDD:cd07765,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1,,,,,,,,LOW,,SNV,5.0,,1,1.0,AAGGTGACTGG,7038f799-3e06-4998-b3c1-69f598faf0b4,836fb985-3ef2-4bd1-9e7c-092e897499f8,0aecac64-5982-4d76-8f31-958f6a00951d,,COSM3861310,N,Unknown,,,,muse;mutect2;varscan2
RING1,6015,BI,GRCh38,chr6,33209959,33209959,+,Missense_Mutation,SNP,G,G,A,rs1204881780,,TCGA-CD-5802-01A-11D-1600-08,TCGA-CD-5802-10A-01D-1600-08,,,,,,,,,Somatic,,,,,,,c1b44966-0f72-4c4f-8783-ab3ffe7f17b2,af722e36-4912-45c4-b431-a2ceff596bac,c.284G>A,p.Arg95Gln,p.R95Q,ENST00000374656,4/7,51,38,13,67,,,"RING1,missense_variant,p.R95Q,ENST00000374656,NM_002931.4,c.284G>A,MODERATE,YES,deleterious(0),probably_damaging(0.958),1;HSD17B8,downstream_gene_variant,,ENST00000374662,NM_014234.5,,MODIFIER,YES,,,1;MIR219A1,downstream_gene_variant,,ENST00000362166,,,MODIFIER,YES,,,1;RING1,non_coding_transcript_exon_variant,,ENST00000478431,,n.272G>A,MODIFIER,,,,1;HSD17B8,downstream_gene_variant,,ENST00000469186,,,MODIFIER,,,,1",A,ENSG00000204227,ENST00000374656,Transcript,missense_variant,missense_variant,487/1741,284/1221,95/406,R/Q,cGa/cAa,rs1204881780;COSV63002527,,1,RING1,HGNC,HGNC:10018,protein_coding,YES,CCDS34424.1,ENSP00000363787,Q06587.198,A0A1U9X8F2.24,UPI000019273E,Q06587-1,NM_002931.4,NM_002931.4,P1,,deleterious(0),probably_damaging(0.958),4/7,,PANTHER:PTHR46076;PANTHER:PTHR46076:SF5;Gene3D:3.30.40.10;Superfamily:SSF57850,,,,,,,,,,,,,,,,,,,,6.762149951100582e-06,0.0,0.0,6.626029789913446e-05,0.0,0.0,0.0,0.0,0.0,0.0,0.0,,,,0;1,,,,,,,,MODERATE,1.0,SNV,1.0,,0;1,,CAAGCGATCCC,7038f799-3e06-4998-b3c1-69f598faf0b4,836fb985-3ef2-4bd1-9e7c-092e897499f8,0aecac64-5982-4d76-8f31-958f6a00951d,,COSM1077967,N,Unknown,,,,muse;mutect2;varscan2
SMOC2,64094,BI,GRCh38,chr6,168510003,168510003,+,Missense_Mutation,SNP,G,G,T,,,TCGA-CD-5802-01A-11D-1600-08,TCGA-CD-5802-10A-01D-1600-08,,,,,,,,,Somatic,,,,,,,c1b44966-0f72-4c4f-8783-ab3ffe7f17b2,af722e36-4912-45c4-b431-a2ceff596bac,c.173G>T,p.Arg58Met,p.R58M,ENST00000356284,2/13,171,133,38,173,,,"SMOC2,missense_variant,p.R58M,ENST00000354536,NM_022138.3,c.173G>T,MODERATE,YES,deleterious(0),probably_damaging(0.998),1;SMOC2,missense_variant,p.R58M,ENST00000356284,NM_001166412.2,c.173G>T,MODERATE,,deleterious(0),probably_damaging(0.997),1",T,ENSG00000112562,ENST00000356284,Transcript,missense_variant,missense_variant,360/3082,173/1341,58/446,R/M,aGg/aTg,COSV62437532,,1,SMOC2,HGNC,HGNC:20323,protein_coding,,CCDS55076.1,ENSP00000348630,Q9H3U7.167,,UPI00000421E5,Q9H3U7-1,NM_001166412.2,NM_001166412.2,P1,,deleterious(0),probably_damaging(0.997),2/13,,PROSITE_profiles:PS51465;CDD:cd00104;PANTHER:PTHR12352:SF21;PANTHER:PTHR12352;Pfam:PF07648;Gene3D:3.30.60.30;SMART:SM00280;Superfamily:SSF100895,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1,,,,,,,,MODERATE,,SNV,1.0,,1,1.0,CGGAAGGACCT,7038f799-3e06-4998-b3c1-69f598faf0b4,836fb985-3ef2-4bd1-9e7c-092e897499f8,0aecac64-5982-4d76-8f31-958f6a00951d,,COSM3860485,N,Unknown,,,,muse;mutect2;varscan2
RNF216,54476,BI,GRCh38,chr7,5741474,5741474,+,Missense_Mutation,SNP,C,C,A,,,TCGA-CD-5802-01A-11D-1600-08,TCGA-CD-5802-10A-01D-1600-08,,,,,,,,,Somatic,,,,,,,c1b44966-0f72-4c4f-8783-ab3ffe7f17b2,af722e36-4912-45c4-b431-a2ceff596bac,c.372G>T,p.Leu124Phe,p.L124F,ENST00000425013,4/17,581,472,108,662,,,"RNF216,missense_variant,p.L181F,ENST00000389902,NM_207111.4,c.543G>T,MODERATE,YES,tolerated_low_confidence(0.09),benign(0.009),-1;RNF216,missense_variant,p.L124F,ENST00000425013,NM_207116.3&NM_001377156.1,c.372G>T,MODERATE,,tolerated_low_confidence(0.21),benign(0.003),-1;RNF216,missense_variant,p.L124F,ENST00000389900,,c.372G>T,MODERATE,,tolerated(0.1),benign(0.033),-1;RNF216,downstream_gene_variant,,ENST00000411812,,,MODIFIER,,,,-1;RNF216,upstream_gene_variant,,ENST00000479541,,,MODIFIER,,,,-1",A,ENSG00000011275,ENST00000425013,Transcript,missense_variant,missense_variant,597/5639,372/2601,124/866,L/F,ttG/ttT,COSV66290408,,-1,RNF216,HGNC,HGNC:21698,protein_coding,,CCDS34595.1,ENSP00000404602,Q9NWF9.179,,UPI000013D69A,Q9NWF9-2,NM_207116.3;NM_001377156.1,,A2,,tolerated_low_confidence(0.21),benign(0.003),4/17,,PANTHER:PTHR22770;PANTHER:PTHR22770:SF13,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1,,,,,,,,MODERATE,,SNV,1.0,,1,1.0,TCTTCCAAGAT,7038f799-3e06-4998-b3c1-69f598faf0b4,836fb985-3ef2-4bd1-9e7c-092e897499f8,0aecac64-5982-4d76-8f31-958f6a00951d,,COSM3881938,N,Unknown,,,,muse;mutect2;varscan2
CREB5,9586,BI,GRCh38,chr7,28804507,28804507,+,Silent,SNP,C,C,T,rs369220982,,TCGA-CD-5802-01A-11D-1600-08,TCGA-CD-5802-10A-01D-1600-08,,,,,,,,,Somatic,,,,,,,c1b44966-0f72-4c4f-8783-ab3ffe7f17b2,af722e36-4912-45c4-b431-a2ceff596bac,c.1011C>T,p.Thr337=,p.T337=,ENST00000357727,8/11,283,238,44,332,,,"CREB5,synonymous_variant,p.T337=,ENST00000357727,NM_182898.4,c.1011C>T,LOW,YES,,,1;CREB5,synonymous_variant,p.T330=,ENST00000396300,NM_004904.3,c.990C>T,LOW,,,,1;CREB5,synonymous_variant,p.T304=,ENST00000396299,NM_182899.4,c.912C>T,LOW,,,,1;CREB5,synonymous_variant,p.T198=,ENST00000396298,NM_001011666.3,c.594C>T,LOW,,,,1;CREB5,synonymous_variant,p.T304=,ENST00000409603,,c.912C>T,LOW,,,,1;CREB5,synonymous_variant,p.T163=,ENST00000426500,,c.489C>T,LOW,,,,1;CREB5,upstream_gene_variant,,ENST00000498316,,,MODIFIER,,,,1",T,ENSG00000146592,ENST00000357727,Transcript,synonymous_variant,synonymous_variant,1408/8539,1011/1527,337/508,T,acC/acT,rs369220982,,1,CREB5,HGNC,HGNC:16844,protein_coding,YES,CCDS5417.1,ENSP00000350359,Q02930.179,,UPI0000457534,Q02930-1,NM_182898.4,NM_182898.4,A1,,,,8/11,,MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite;PANTHER:PTHR19304:SF8;PANTHER:PTHR19304;PIRSF:PIRSF003153,,,,,,,0.000227,0.0,3.621e-05,0.0001845,5.784e-05,0.0,0.0,0.0,1.802e-05,0.0,6.539e-05,0.000227,AA,0.0001014349982142,0.0002920420083682,0.0,0.0,0.0,0.0,0.0,0.0,3.086610013269819e-05,0.0004950499860569,0.0,0.0002920420083682,afr,,,,,,,,,,LOW,1.0,SNV,1.0,,,,CACACCGGCAA,7038f799-3e06-4998-b3c1-69f598faf0b4,836fb985-3ef2-4bd1-9e7c-092e897499f8,0aecac64-5982-4d76-8f31-958f6a00951d,,COSM301992;COSM301993,N,Unknown,,,,muse;mutect2;varscan2
ESCO2,157570,BI,GRCh38,chr8,27803390,27803390,+,Silent,SNP,C,C,G,,,TCGA-CD-5802-01A-11D-1600-08,TCGA-CD-5802-10A-01D-1600-08,,,,,,,,,Somatic,,,,,,,c1b44966-0f72-4c4f-8783-ab3ffe7f17b2,af722e36-4912-45c4-b431-a2ceff596bac,c.1758C>G,p.Thr586=,p.T586=,ENST00000305188,11/11,249,206,43,270,,,"ESCO2,synonymous_variant,p.T586=,ENST00000305188,NM_001017420.3,c.1758C>G,LOW,YES,,,1;ESCO2,intron_variant,,ENST00000397418,,c.685+17C>G,MODIFIER,,,,1;ESCO2,downstream_gene_variant,,ENST00000518262,,,MODIFIER,,,,1;ESCO2,intron_variant,,ENST00000522378,,c.*716+17C>G,MODIFIER,,,,1",G,ENSG00000171320,ENST00000305188,Transcript,synonymous_variant,synonymous_variant,1828/3754,1758/1806,586/601,T,acC/acG,COSV59414467,,1,ESCO2,HGNC,HGNC:27230,protein_coding,YES,CCDS34872.1,ENSP00000306999,Q56NI9.131,,UPI0000160D17,Q56NI9-1,NM_001017420.3,NM_001017420.3,P1,,,,11/11,,Pfam:PF13880;PANTHER:PTHR45884;PANTHER:PTHR45884:SF3,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1,,,,,,,,LOW,1.0,SNV,1.0,,1,1.0,GCAACCAAGTA,7038f799-3e06-4998-b3c1-69f598faf0b4,836fb985-3ef2-4bd1-9e7c-092e897499f8,0aecac64-5982-4d76-8f31-958f6a00951d,,COSM3899328,N,Unknown,,,,muse;mutect2;varscan2
TTI2,80185,BI,GRCh38,chr8,33513512,33513512,+,5'Flank,SNP,C,C,T,rs185083029,,TCGA-CD-5802-01A-11D-1600-08,TCGA-CD-5802-10A-01D-1600-08,,,,,,,,,Somatic,,,,,,,c1b44966-0f72-4c4f-8783-ab3ffe7f17b2,af722e36-4912-45c4-b431-a2ceff596bac,,,,ENST00000360742,,241,189,52,290,,,"TTI2,upstream_gene_variant,,ENST00000360742,,,MODIFIER,,,,-1;TTI2,upstream_gene_variant,,ENST00000431156,NM_001102401.4&NM_025115.5,,MODIFIER,,,,-1;TTI2,upstream_gene_variant,,ENST00000520636,NM_001330505.3,,MODIFIER,,,,-1;TTI2,upstream_gene_variant,,ENST00000523305,,,MODIFIER,,,,-1;TTI2,upstream_gene_variant,,ENST00000613904,NM_001265581.2,,MODIFIER,YES,,,-1;SNORD13,non_coding_transcript_exon_variant,,ENST00000459299,,n.38C>T,MODIFIER,YES,,,1;TTI2,upstream_gene_variant,,ENST00000519356,,,MODIFIER,,,,-1",T,ENSG00000129696,ENST00000360742,Transcript,upstream_gene_variant,upstream_gene_variant,,,,,,rs185083029;COSV100659807,403.0,-1,TTI2,HGNC,HGNC:26262,protein_coding,,CCDS6090.1,ENSP00000353971,Q6NXR4.124,,UPI000013D26B,,,,P1,,,,,,,,,,,,,,,2.614e-05,0.0,0.0,0.0,5.692e-05,0.0,2.828e-05,0.0,6.598e-05,6.598e-05,gnomAD_SAS,3.380710040801205e-05,4.864290167461149e-05,0.0,0.0,0.0,0.0002014500059885,0.0,0.0,3.086229844484478e-05,0.0,0.0,4.864290167461149e-05,afr,,0;1,,,,,,,,MODIFIER,,SNV,2.0,,0;1,1.0,GTGTTCATACG,7038f799-3e06-4998-b3c1-69f598faf0b4,836fb985-3ef2-4bd1-9e7c-092e897499f8,0aecac64-5982-4d76-8f31-958f6a00951d,,,N,Unknown,,,,muse;mutect2;varscan2
SULF1,23213,BI,GRCh38,chr8,69624074,69624074,+,Missense_Mutation,SNP,G,G,A,rs758690728,,TCGA-CD-5802-01A-11D-1600-08,TCGA-CD-5802-10A-01D-1600-08,,,,,,,,,Somatic,,,,,,,c1b44966-0f72-4c4f-8783-ab3ffe7f17b2,af722e36-4912-45c4-b431-a2ceff596bac,c.1727G>A,p.Arg576His,p.R576H,ENST00000260128,15/23,102,81,21,106,,,"SULF1,missense_variant,p.R576H,ENST00000260128,NM_015170.2,c.1727G>A,MODERATE,YES,deleterious(0.03),probably_damaging(0.999),1;SULF1,missense_variant,p.R576H,ENST00000402687,NM_001128205.2,c.1727G>A,MODERATE,,deleterious(0.03),probably_damaging(0.999),1;SULF1,missense_variant,p.R576H,ENST00000458141,NM_001128204.2,c.1727G>A,MODERATE,,deleterious(0.03),probably_damaging(0.999),1;SULF1,missense_variant,p.R576H,ENST00000419716,NM_001128206.2,c.1727G>A,MODERATE,,deleterious(0.03),probably_damaging(0.999),1;SULF1,missense_variant,p.R360H,ENST00000616868,,c.1079G>A,MODERATE,,deleterious(0.03),benign(0.345),1;SULF1,non_coding_transcript_exon_variant,,ENST00000521946,,n.1067G>A,MODIFIER,,,,1;SULF1,upstream_gene_variant,,ENST00000524731,,,MODIFIER,,,,1;SULF1,upstream_gene_variant,,ENST00000531512,,,MODIFIER,,,,1",A,ENSG00000137573,ENST00000260128,Transcript,missense_variant,missense_variant,2444/5710,1727/2616,576/871,R/H,cGt/cAt,rs758690728;COSV52674097,,1,SULF1,HGNC,HGNC:20391,protein_coding,YES,CCDS6204.1,ENSP00000260128,Q8IWU6.143,A0A024R809.49,UPI000003FD82,,NM_015170.2,,P1,,deleterious(0.03),probably_damaging(0.999),15/23,,PIRSF:PIRSF036665;Pfam:PF12548;PANTHER:PTHR43108;PANTHER:PTHR43108:SF1;MobiDB_lite:mobidb-lite,,,,,,,,,0.0001472,0.0003079,0.0001158,0.0,0.0,0.0,0.0001408,0.000163,0.0003593,0.0003593,gnomAD_SAS,9.461509762331843e-05,7.293240196304396e-05,0.0,6.622519867960364e-05,0.0,0.0,0.0,0.0,0.0001080049987649,0.0,0.0006249999860301,0.0006249999860301,sas,,0;1,,,,,,,,MODERATE,1.0,SNV,5.0,,0;1,,TAAGCGTCATG,7038f799-3e06-4998-b3c1-69f598faf0b4,836fb985-3ef2-4bd1-9e7c-092e897499f8,0aecac64-5982-4d76-8f31-958f6a00951d,,COSM3413099,N,Unknown,,,,muse;mutect2;varscan2
FREM1,158326,BI,GRCh38,chr9,14748596,14748596,+,Silent,SNP,G,G,A,,,TCGA-CD-5802-01A-11D-1600-08,TCGA-CD-5802-10A-01D-1600-08,,,,,,,,,Somatic,,,,,,,c1b44966-0f72-4c4f-8783-ab3ffe7f17b2,af722e36-4912-45c4-b431-a2ceff596bac,c.5601C>T,p.Ser1867=,p.S1867=,ENST00000380880,31/37,427,346,81,483,,,"FREM1,synonymous_variant,p.S1867=,ENST00000380880,NM_144966.7&NM_001379081.2,c.5601C>T,LOW,YES,,,-1;FREM1,synonymous_variant,p.S403=,ENST00000380894,NM_001370061.2&NM_001370058.2&NM_001177704.3,c.1209C>T,LOW,,,,-1;FREM1,downstream_gene_variant,,ENST00000486223,,,MODIFIER,,,,-1;FREM1,3_prime_UTR_variant,,ENST00000380875,,c.*167C>T,MODIFIER,,,,-1;FREM1,intron_variant,,ENST00000427623,,c.647-868C>T,MODIFIER,,,,-1",A,ENSG00000164946,ENST00000380880,Transcript,synonymous_variant,synonymous_variant,6383/7566,5601/6540,1867/2179,S,agC/agT,COSV66523112,,-1,FREM1,HGNC,HGNC:23399,protein_coding,YES,CCDS47952.1,ENSP00000370262,Q5H8C1.151,,UPI000057A218,Q5H8C1-1,NM_144966.7;NM_001379081.2,NM_001379081.2,P1,,,,31/37,,PANTHER:PTHR45739;PANTHER:PTHR45739:SF7,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1,,,,,,,,LOW,1.0,SNV,5.0,,1,1.0,CATGTGCTGTG,7038f799-3e06-4998-b3c1-69f598faf0b4,836fb985-3ef2-4bd1-9e7c-092e897499f8,0aecac64-5982-4d76-8f31-958f6a00951d,,COSM3090184;COSM3090185,N,Unknown,,,,muse;mutect2;varscan2
C9orf131,138724,BI,GRCh38,chr9,35045808,35045808,+,Missense_Mutation,SNP,A,A,G,,,TCGA-CD-5802-01A-11D-1600-08,TCGA-CD-5802-10A-01D-1600-08,,,,,,,,,Somatic,,,,,,,c1b44966-0f72-4c4f-8783-ab3ffe7f17b2,af722e36-4912-45c4-b431-a2ceff596bac,c.3179A>G,p.Gln1060Arg,p.Q1060R,ENST00000312292,2/2,272,214,57,357,,,"C9orf131,missense_variant,p.Q1060R,ENST00000312292,NM_001287391.2&NM_203299.4&NM_001040410.3,c.3179A>G,MODERATE,YES,tolerated(0.05),probably_damaging(0.943),1;C9orf131,missense_variant,p.Q1012R,ENST00000421362,NM_001040412.2,c.3035A>G,MODERATE,,tolerated(0.05),probably_damaging(0.943),1;C9orf131,missense_variant,p.Q987R,ENST00000354479,NM_001040411.2,c.2960A>G,MODERATE,,tolerated(0.05),possibly_damaging(0.9),1;C9orf131,downstream_gene_variant,,ENST00000378745,,,MODIFIER,,,,1;C9orf131,downstream_gene_variant,,ENST00000534880,,,MODIFIER,,,,1;C9orf131,downstream_gene_variant,,ENST00000537671,,,MODIFIER,,,,1;RN7SL338P,upstream_gene_variant,,ENST00000481467,,,MODIFIER,YES,,,1;AL353795.3,upstream_gene_variant,,ENST00000624351,,,MODIFIER,YES,,,-1;C9orf131,downstream_gene_variant,,ENST00000416537,,,MODIFIER,,,,1",G,ENSG00000174038,ENST00000312292,Transcript,missense_variant,missense_variant,3194/3372,3179/3240,1060/1079,Q/R,cAa/cGa,COSV56611041,,1,C9orf131,HGNC,HGNC:31418,protein_coding,YES,CCDS6572.2,ENSP00000308279,Q5VYM1.105,,UPI00001605AC,Q5VYM1-1,NM_001287391.2;NM_203299.4;NM_001040410.3,NM_203299.4,P4,,tolerated(0.05),probably_damaging(0.943),2/2,,PANTHER:PTHR21777,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1,,,,,,,,MODERATE,1.0,SNV,1.0,,1,,TTTGCAAAAGG,7038f799-3e06-4998-b3c1-69f598faf0b4,836fb985-3ef2-4bd1-9e7c-092e897499f8,0aecac64-5982-4d76-8f31-958f6a00951d,,COSM3907070;COSM3907071,N,Unknown,,,,muse;mutect2;varscan2
USP54,159195,BI,GRCh38,chr10,73498805,73498805,+,Nonsense_Mutation,SNP,G,G,A,rs779266508,,TCGA-CD-5802-01A-11D-1600-08,TCGA-CD-5802-10A-01D-1600-08,,,,,,,,,Somatic,,,,,,,c1b44966-0f72-4c4f-8783-ab3ffe7f17b2,af722e36-4912-45c4-b431-a2ceff596bac,c.4879C>T,p.Arg1627Ter,p.R1627*,ENST00000339859,23/23,135,102,33,213,,,"USP54,stop_gained,p.R1627*,ENST00000339859,NM_152586.4&NM_001350995.2&NM_001378208.1&NM_001378209.1&NM_001320437.2&NM_001378210.1,c.4879C>T,HIGH,YES,,,-1;USP54,stop_gained,p.R668*,ENST00000422491,,c.2002C>T,HIGH,,,,-1;PPP3CB,upstream_gene_variant,,ENST00000342558,NM_001289968.1&NM_001289969.1,,MODIFIER,,,,-1;PPP3CB,upstream_gene_variant,,ENST00000360663,NM_021132.4,,MODIFIER,,,,-1;PPP3CB,upstream_gene_variant,,ENST00000394828,NM_001142354.2,,MODIFIER,,,,-1;PPP3CB,upstream_gene_variant,,ENST00000394829,NM_001142353.2,,MODIFIER,YES,,,-1;USP54,non_coding_transcript_exon_variant,,ENST00000497106,,n.4263C>T,MODIFIER,,,,-1;USP54,3_prime_UTR_variant,,ENST00000424265,,c.*2028C>T,MODIFIER,,,,-1;USP54,3_prime_UTR_variant,,ENST00000466048,,c.*2169C>T,MODIFIER,,,,-1;USP54,3_prime_UTR_variant,,ENST00000418501,,c.*2028C>T,MODIFIER,,,,-1;PPP3CB-AS1,non_coding_transcript_exon_variant,,ENST00000439792,,n.250G>A,MODIFIER,,,,1;USP54,downstream_gene_variant,,ENST00000464635,,,MODIFIER,,,,-1;PPP3CB-AS1,non_coding_transcript_exon_variant,,ENST00000620302,,n.903G>A,MODIFIER,YES,,,1;PPP3CB-AS1,non_coding_transcript_exon_variant,,ENST00000620559,,n.1370G>A,MODIFIER,,,,1;PPP3CB-AS1,non_coding_transcript_exon_variant,,ENST00000596320,,n.270G>A,MODIFIER,,,,1;PPP3CB-AS1,non_coding_transcript_exon_variant,,ENST00000593790,,n.349G>A,MODIFIER,,,,1;PPP3CB-AS1,non_coding_transcript_exon_variant,,ENST00000610317,,n.267G>A,MODIFIER,,,,1;PPP3CB-AS1,non_coding_transcript_exon_variant,,ENST00000620432,,n.548G>A,MODIFIER,,,,1;PPP3CB-AS1,intron_variant,,ENST00000422977,,n.1059-790G>A,MODIFIER,,,,1;PPP3CB-AS1,intron_variant,,ENST00000442133,,n.440-790G>A,MODIFIER,,,,1;PPP3CB-AS1,intron_variant,,ENST00000595069,,n.195-790G>A,MODIFIER,,,,1;PPP3CB-AS1,intron_variant,,ENST00000595935,,n.299-790G>A,MODIFIER,,,,1;PPP3CB-AS1,intron_variant,,ENST00000597958,,n.198-790G>A,MODIFIER,,,,1;PPP3CB-AS1,intron_variant,,ENST00000600206,,n.198-790G>A,MODIFIER,,,,1;PPP3CB-AS1,intron_variant,,ENST00000600607,,n.612-790G>A,MODIFIER,,,,1;PPP3CB-AS1,intron_variant,,ENST00000600887,,n.158-790G>A,MODIFIER,,,,1",A,ENSG00000166348,ENST00000339859,Transcript,stop_gained,stop_gained,4980/6247,4879/5055,1627/1684,R/*,Cga/Tga,rs779266508;COSV60442351,,-1,USP54,HGNC,HGNC:23513,protein_coding,YES,CCDS7329.2,ENSP00000345216,Q70EL1.126,,UPI0000DFF136,Q70EL1-1,NM_152586.4;NM_001350995.2;NM_001378208.1;NM_001378209.1;NM_001320437.2;NM_001378210.1,,P1,,,,23/23,,MobiDB_lite:mobidb-lite,,,,,,,,,1.198e-05,0.0,0.0,0.0,5.437e-05,0.0,8.836e-06,0.0,3.285e-05,5.437e-05,gnomAD_EAS,6.770109848730499e-06,0.0,0.0,0.0,0.0,0.0,0.0,0.0,1.544070073578041e-05,0.0,0.0,,,,0;1,,,,,,,,HIGH,,SNV,5.0,,0;1,,GGTTCGGGACC,7038f799-3e06-4998-b3c1-69f598faf0b4,836fb985-3ef2-4bd1-9e7c-092e897499f8,0aecac64-5982-4d76-8f31-958f6a00951d,,COSM4015737;COSM4015738,N,Unknown,,,,muse;mutect2;varscan2
PRR5L,79899,BI,GRCh38,chr11,36462605,36462605,+,Missense_Mutation,SNP,C,C,A,,,TCGA-CD-5802-01A-11D-1600-08,TCGA-CD-5802-10A-01D-1600-08,,,,,,,,,Somatic,,,,,,,c1b44966-0f72-4c4f-8783-ab3ffe7f17b2,af722e36-4912-45c4-b431-a2ceff596bac,c.976C>A,p.Pro326Thr,p.P326T,ENST00000378867,10/10,36,28,7,52,,,"PRR5L,missense_variant,p.P326T,ENST00000378867,NM_024841.4,c.976C>A,MODERATE,YES,deleterious(0.04),benign(0.115),1;PRR5L,missense_variant,p.P326T,ENST00000530639,NM_001160167.2,c.976C>A,MODERATE,,deleterious(0.04),benign(0.115),1;PRR5L,downstream_gene_variant,,ENST00000527487,NM_001160169.1,,MODIFIER,,,,1;PRR5L,non_coding_transcript_exon_variant,,ENST00000389693,NM_001160168.1,n.711C>A,MODIFIER,,,,1;PRR5L,non_coding_transcript_exon_variant,,ENST00000530627,,n.422C>A,MODIFIER,,,,1;PRR5L,non_coding_transcript_exon_variant,,ENST00000525672,,n.421C>A,MODIFIER,,,,1;PRR5L,non_coding_transcript_exon_variant,,ENST00000529020,,n.477C>A,MODIFIER,,,,1",A,ENSG00000135362,ENST00000378867,Transcript,missense_variant,missense_variant,1331/3930,976/1107,326/368,P/T,Cca/Aca,COSV100287068;COSV61121294,,1,PRR5L,HGNC,HGNC:25878,protein_coding,YES,CCDS31463.1,ENSP00000368144,Q6MZQ0.110,,UPI0000DBEF36,Q6MZQ0-1,NM_024841.4,,P2,,deleterious(0.04),benign(0.115),10/10,,PANTHER:PTHR32428:SF3;PANTHER:PTHR32428,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1;1,,,,,,,,MODERATE,1.0,SNV,1.0,,1;1,,TCCTGCCACCC,7038f799-3e06-4998-b3c1-69f598faf0b4,836fb985-3ef2-4bd1-9e7c-092e897499f8,0aecac64-5982-4d76-8f31-958f6a00951d,,COSM4032605,N,Unknown,,,,muse;mutect2
ARFGAP2,84364,BI,GRCh38,chr11,47175282,47175282,+,Missense_Mutation,SNP,G,G,C,rs1432651459,,TCGA-CD-5802-01A-11D-1600-08,TCGA-CD-5802-10A-01D-1600-08,,,,,,,,,Somatic,,,,,,,c1b44966-0f72-4c4f-8783-ab3ffe7f17b2,af722e36-4912-45c4-b431-a2ceff596bac,c.296C>G,p.Ala99Gly,p.A99G,ENST00000524782,4/16,236,190,46,232,,,"ARFGAP2,missense_variant,p.A99G,ENST00000426335,NM_001242832.1,c.296C>G,MODERATE,,deleterious(0.05),benign(0.078),-1;ARFGAP2,missense_variant,p.A99G,ENST00000524782,NM_032389.6,c.296C>G,MODERATE,YES,deleterious(0),benign(0.111),-1;ARFGAP2,missense_variant,p.A99G,ENST00000525398,,c.296C>G,MODERATE,,deleterious(0.03),benign(0.043),-1;ARFGAP2,missense_variant,p.A99G,ENST00000525314,,c.296C>G,MODERATE,,deleterious(0.02),benign(0.037),-1;ARFGAP2,missense_variant,p.A99G,ENST00000528444,,c.296C>G,MODERATE,,deleterious(0.01),benign(0.123),-1;ARFGAP2,missense_variant,p.A92G,ENST00000530596,,c.275C>G,MODERATE,,deleterious(0.02),benign(0.059),-1;ARFGAP2,intron_variant,,ENST00000526342,,c.191+1234C>G,MODIFIER,,,,-1;ARFGAP2,intron_variant,,ENST00000527927,,c.264+569C>G,MODIFIER,,,,-1;ARFGAP2,intron_variant,,ENST00000627920,,c.264+569C>G,MODIFIER,,,,-1;ARFGAP2,intron_variant,,ENST00000629231,,c.191+1234C>G,MODIFIER,,,,-1;PACSIN3,downstream_gene_variant,,ENST00000298838,NM_001184974.2&NM_016223.5,,MODIFIER,,,,-1;ARFGAP2,upstream_gene_variant,,ENST00000527776,,,MODIFIER,,,,-1;PACSIN3,downstream_gene_variant,,ENST00000528201,,,MODIFIER,,,,-1;PACSIN3,downstream_gene_variant,,ENST00000528462,,,MODIFIER,,,,-1;PACSIN3,downstream_gene_variant,,ENST00000530513,,,MODIFIER,,,,-1;PACSIN3,downstream_gene_variant,,ENST00000533686,,,MODIFIER,,,,-1;PACSIN3,downstream_gene_variant,,ENST00000539589,NM_001184975.1,,MODIFIER,YES,,,-1;MIR6745,downstream_gene_variant,,ENST00000612694,,,MODIFIER,YES,,,-1;ARFGAP2,non_coding_transcript_exon_variant,,ENST00000395449,,n.302C>G,MODIFIER,,,,-1;ARFGAP2,non_coding_transcript_exon_variant,,ENST00000531750,,n.323C>G,MODIFIER,,,,-1;ARFGAP2,non_coding_transcript_exon_variant,,ENST00000533939,,n.290C>G,MODIFIER,,,,-1;ARFGAP2,non_coding_transcript_exon_variant,,ENST00000529599,,n.322C>G,MODIFIER,,,,-1;ARFGAP2,missense_variant,p.A57G,ENST00000532478,,c.170C>G,MODERATE,,deleterious(0.03),possibly_damaging(0.64),-1;ARFGAP2,missense_variant,p.A99G,ENST00000529455,,c.296C>G,MODERATE,,tolerated(0.37),benign(0.043),-1;ARFGAP2,missense_variant,p.P75A,ENST00000528041,,c.223C>G,MODERATE,,deleterious_low_confidence(0),benign(0),-1;ARFGAP2,3_prime_UTR_variant,,ENST00000529439,,c.*323C>G,MODIFIER,,,,-1;ARFGAP2,3_prime_UTR_variant,,ENST00000528708,,c.*323C>G,MODIFIER,,,,-1;ARFGAP2,3_prime_UTR_variant,,ENST00000524586,,c.*111C>G,MODIFIER,,,,-1;ARFGAP2,non_coding_transcript_exon_variant,,ENST00000526185,,n.848C>G,MODIFIER,,,,-1;ARFGAP2,non_coding_transcript_exon_variant,,ENST00000524727,,n.302C>G,MODIFIER,,,,-1;ARFGAP2,non_coding_transcript_exon_variant,,ENST00000527097,,n.311C>G,MODIFIER,,,,-1;ARFGAP2,non_coding_transcript_exon_variant,,ENST00000530794,,n.323C>G,MODIFIER,,,,-1;ARFGAP2,intron_variant,,ENST00000532438,,c.264+569C>G,MODIFIER,,,,-1;ARFGAP2,intron_variant,,ENST00000533243,,c.191+1234C>G,MODIFIER,,,,-1;ARFGAP2,upstream_gene_variant,,ENST00000526948,,,MODIFIER,,,,-1;ARFGAP2,downstream_gene_variant,,ENST00000528072,,,MODIFIER,,,,-1;PACSIN3,downstream_gene_variant,,ENST00000532457,,,MODIFIER,,,,-1",C,ENSG00000149182,ENST00000524782,Transcript,missense_variant,missense_variant,322/2773,296/1566,99/521,A/G,gCc/gGc,rs1432651459;COSV54066033,,-1,ARFGAP2,HGNC,HGNC:13504,protein_coding,YES,CCDS7926.1,ENSP00000434442,Q8N6H7.150,,UPI000006F4C6,Q8N6H7-1,NM_032389.6,NM_032389.6,P1,,deleterious(0),benign(0.111),4/16,,PDB-ENSP_mappings:2p57.A;Gene3D:3.30.40.160;Pfam:PF01412;PROSITE_profiles:PS50115;PANTHER:PTHR45686;PANTHER:PTHR45686:SF10;SMART:SM00105;Superfamily:SSF57863;CDD:cd09029,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,0;1,,,,,,,,MODERATE,1.0,SNV,1.0,,0;1,,CATTGGCTGTG,7038f799-3e06-4998-b3c1-69f598faf0b4,836fb985-3ef2-4bd1-9e7c-092e897499f8,0aecac64-5982-4d76-8f31-958f6a00951d,,COSM4033126,N,Unknown,,,,muse;mutect2;varscan2
MS4A14,84689,BI,GRCh38,chr11,60416217,60416217,+,Missense_Mutation,SNP,C,C,T,,,TCGA-CD-5802-01A-11D-1600-08,TCGA-CD-5802-10A-01D-1600-08,,,,,,,,,Somatic,,,,,,,c1b44966-0f72-4c4f-8783-ab3ffe7f17b2,af722e36-4912-45c4-b431-a2ceff596bac,c.1249C>T,p.Pro417Ser,p.P417S,ENST00000300187,5/5,80,56,23,121,,,"MS4A14,missense_variant,p.P433S,ENST00000395001,NM_001261827.1,c.1297C>T,MODERATE,,tolerated(0.41),benign(0.018),1;MS4A14,missense_variant,p.P450S,ENST00000531783,NM_001261828.2,c.1348C>T,MODERATE,YES,tolerated(0.41),benign(0.007),1;MS4A14,missense_variant,p.P417S,ENST00000300187,NM_032597.5,c.1249C>T,MODERATE,,tolerated(0.41),benign(0.346),1;MS4A14,missense_variant,p.P400S,ENST00000395005,NM_001079692.3,c.1198C>T,MODERATE,,tolerated(0.41),possibly_damaging(0.451),1;MS4A14,missense_variant,p.P305S,ENST00000531787,,c.913C>T,MODERATE,,tolerated(0.42),benign(0.346),1;MS4A14,3_prime_UTR_variant,,ENST00000530662,,c.*956C>T,MODIFIER,,,,1;MS4A14,3_prime_UTR_variant,,ENST00000527841,,c.*857C>T,MODIFIER,,,,1;MS4A14,3_prime_UTR_variant,,ENST00000525397,,c.*857C>T,MODIFIER,,,,1",T,ENSG00000166928,ENST00000300187,Transcript,missense_variant,missense_variant,1369/2908,1249/2040,417/679,P/S,Cct/Tct,COSV55734768;COSV99038259,,1,MS4A14,HGNC,HGNC:30706,protein_coding,,CCDS31569.1,ENSP00000300187,Q96JA4.123,,UPI000013E636,Q96JA4-1,NM_032597.5,NM_032597.5,A2,,tolerated(0.41),benign(0.346),5/5,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1;1,,,,,,,,MODERATE,,SNV,1.0,,1;1,,TATTACCTGAA,7038f799-3e06-4998-b3c1-69f598faf0b4,836fb985-3ef2-4bd1-9e7c-092e897499f8,0aecac64-5982-4d76-8f31-958f6a00951d,,COSM4034418,N,Unknown,,,,muse;mutect2;varscan2
FIBP,9158,BI,GRCh38,chr11,65887950,65887950,+,Missense_Mutation,SNP,C,C,T,rs766679393,,TCGA-CD-5802-01A-11D-1600-08,TCGA-CD-5802-10A-01D-1600-08,,,,,,,,,Somatic,,,,,,,c1b44966-0f72-4c4f-8783-ab3ffe7f17b2,af722e36-4912-45c4-b431-a2ceff596bac,c.268G>A,p.Ala90Thr,p.A90T,ENST00000338369,2/10,23,18,5,43,,,"FIBP,missense_variant,p.A90T,ENST00000357519,NM_004214.5,c.268G>A,MODERATE,,tolerated(0.58),benign(0.001),-1;FIBP,missense_variant,p.A90T,ENST00000338369,NM_198897.2,c.268G>A,MODERATE,YES,tolerated(0.58),benign(0.005),-1;FIBP,missense_variant,p.A87T,ENST00000533045,,c.259G>A,MODERATE,,tolerated(0.58),benign(0.003),-1;CTSW,downstream_gene_variant,,ENST00000307886,NM_001335.4,,MODIFIER,YES,,,1;FOSL1,downstream_gene_variant,,ENST00000312562,NM_001300856.2&NM_005438.5,,MODIFIER,YES,,,-1;CCDC85B,upstream_gene_variant,,ENST00000312579,NM_006848.3,,MODIFIER,YES,,,1;FOSL1,downstream_gene_variant,,ENST00000448083,NM_001300857.2,,MODIFIER,,,,-1;CTSW,downstream_gene_variant,,ENST00000528419,,,MODIFIER,,,,1;FOSL1,downstream_gene_variant,,ENST00000531493,NM_001300844.2,,MODIFIER,,,,-1;FOSL1,downstream_gene_variant,,ENST00000532401,NM_001300855.2,,MODIFIER,,,,-1;FIBP,non_coding_transcript_exon_variant,,ENST00000426652,,n.311G>A,MODIFIER,,,,-1;FIBP,missense_variant,p.A90T,ENST00000533037,,c.268G>A,MODERATE,,tolerated(0.58),benign(0.005),-1;FIBP,missense_variant,p.A90T,ENST00000532229,,c.268G>A,MODERATE,,tolerated(0.58),benign(0.005),-1;FIBP,non_coding_transcript_exon_variant,,ENST00000528937,,n.363G>A,MODIFIER,,,,-1;FIBP,non_coding_transcript_exon_variant,,ENST00000532679,,n.311G>A,MODIFIER,,,,-1;FIBP,non_coding_transcript_exon_variant,,ENST00000442885,,n.360G>A,MODIFIER,,,,-1;FIBP,upstream_gene_variant,,ENST00000525765,,,MODIFIER,,,,-1;FIBP,upstream_gene_variant,,ENST00000531115,,,MODIFIER,,,,-1;FIBP,upstream_gene_variant,,ENST00000532934,,,MODIFIER,,,,-1;FIBP,upstream_gene_variant,,ENST00000534032,,,MODIFIER,,,,-1",T,ENSG00000172500,ENST00000338369,Transcript,missense_variant,missense_variant,381/1261,268/1095,90/364,A/T,Gca/Aca,rs766679393;COSV57027948;COSV57029414,,-1,FIBP,HGNC,HGNC:3705,protein_coding,YES,CCDS8119.1,ENSP00000344572,O43427.169,,UPI000012A79E,O43427-1,NM_198897.2,,,,tolerated(0.58),benign(0.005),2/10,,Pfam:PF05427;PANTHER:PTHR13223,,,,,,,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS,6.757029950676952e-06,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0002082470018649,,,,0;1;1,,,,,,,,MODERATE,1.0,SNV,1.0,,0;1;1,1.0,TAGTGCCTGCC,7038f799-3e06-4998-b3c1-69f598faf0b4,836fb985-3ef2-4bd1-9e7c-092e897499f8,0aecac64-5982-4d76-8f31-958f6a00951d,,COSM4035583,N,Unknown,,,,muse;mutect2;varscan2
WNK1,65125,BI,GRCh38,chr12,896132,896132,+,Missense_Mutation,SNP,C,C,T,,,TCGA-CD-5802-01A-11D-1600-08,TCGA-CD-5802-10A-01D-1600-08,,,,,,,,,Somatic,,,,,,,c1b44966-0f72-4c4f-8783-ab3ffe7f17b2,af722e36-4912-45c4-b431-a2ceff596bac,c.5645C>T,p.Ser1882Phe,p.S1882F,ENST00000315939,24/28,198,178,20,159,,,"WNK1,missense_variant,p.S2295F,ENST00000530271,,c.6884C>T,MODERATE,YES,deleterious(0.01),probably_damaging(0.987),1;WNK1,missense_variant,p.S2142F,ENST00000537687,NM_001184985.1,c.6425C>T,MODERATE,,deleterious(0.01),possibly_damaging(0.858),1;WNK1,missense_variant,p.S2134F,ENST00000340908,NM_213655.4,c.6401C>T,MODERATE,,deleterious(0.01),possibly_damaging(0.858),1;WNK1,missense_variant,p.S1882F,ENST00000315939,NM_018979.4,c.5645C>T,MODERATE,,deleterious(0.01),possibly_damaging(0.726),1;WNK1,missense_variant,p.S1634F,ENST00000535572,NM_014823.3,c.4901C>T,MODERATE,,deleterious(0.02),possibly_damaging(0.858),1;WNK1,missense_variant,p.S1475F,ENST00000675631,,c.4424C>T,MODERATE,,deleterious(0.01),probably_damaging(0.953),1;WNK1,missense_variant,p.S1031F,ENST00000676347,,c.3092C>T,MODERATE,,deleterious(0.02),probably_damaging(0.924),1;WNK1,upstream_gene_variant,,ENST00000544559,,,MODIFIER,,,,1;WNK1,upstream_gene_variant,,ENST00000537603,,,MODIFIER,,,,1;WNK1,upstream_gene_variant,,ENST00000542424,,,MODIFIER,,,,1",T,ENSG00000060237,ENST00000315939,Transcript,missense_variant,missense_variant,6632/10796,5645/7149,1882/2382,S/F,tCt/tTt,COSV60032644,,1,WNK1,HGNC,HGNC:14540,protein_coding,,CCDS8506.1,ENSP00000313059,Q9H4A3.203,,UPI000013CD65,,NM_018979.4,NM_018979.4,A2,,deleterious(0.01),possibly_damaging(0.726),24/28,,PANTHER:PTHR13902;PANTHER:PTHR13902:SF46;MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1,,,,,,,,MODERATE,,SNV,1.0,,1,1.0,AAAGTCTGTTC,7038f799-3e06-4998-b3c1-69f598faf0b4,836fb985-3ef2-4bd1-9e7c-092e897499f8,0aecac64-5982-4d76-8f31-958f6a00951d,,COSM4037876;COSM4037877,N,Unknown,,,,muse;mutect2;varscan2
GALNT8,26290,BI,GRCh38,chr12,4744660,4744660,+,Missense_Mutation,SNP,G,G,A,rs886503126,,TCGA-CD-5802-01A-11D-1600-08,TCGA-CD-5802-10A-01D-1600-08,,,,,,,,,Somatic,,,,,,,c1b44966-0f72-4c4f-8783-ab3ffe7f17b2,af722e36-4912-45c4-b431-a2ceff596bac,c.820G>A,p.Val274Ile,p.V274I,ENST00000252318,4/11,73,46,27,72,,,"GALNT8,missense_variant,p.V274I,ENST00000252318,NM_017417.2,c.820G>A,MODERATE,YES,tolerated(0.06),possibly_damaging(0.463),1;AC005833.1,intron_variant,,ENST00000648836,,c.964-16298G>A,MODIFIER,YES,,,1;GALNT8,upstream_gene_variant,,ENST00000648865,,,MODIFIER,,,,1;AC005833.1,downstream_gene_variant,,ENST00000544741,,,MODIFIER,,,,1",A,ENSG00000130035,ENST00000252318,Transcript,missense_variant,missense_variant,1098/2321,820/1914,274/637,V/I,Gtc/Atc,rs886503126;COSV52897273,,1,GALNT8,HGNC,HGNC:4130,protein_coding,YES,CCDS8533.1,ENSP00000252318,Q9NY28.144,,UPI0000070DEC,,NM_017417.2,NM_017417.2,P1,,tolerated(0.06),possibly_damaging(0.463),4/11,,Gene3D:3.90.550.10;Pfam:PF00535;PANTHER:PTHR11675;PANTHER:PTHR11675:SF50;Superfamily:SSF53448;CDD:cd02510,,,,,,,,,,,,,,,,,,,,2.703360041778069e-05,9.72479028860107e-05,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,9.72479028860107e-05,afr,,0;1,,,,,,,,MODERATE,1.0,SNV,1.0,,0;1,,ACGTGGTCGCC,7038f799-3e06-4998-b3c1-69f598faf0b4,836fb985-3ef2-4bd1-9e7c-092e897499f8,0aecac64-5982-4d76-8f31-958f6a00951d,,COSM4042209,N,Unknown,,,,muse;mutect2;varscan2
GSG1,83445,BI,GRCh38,chr12,13088864,13088864,+,Missense_Mutation,SNP,C,C,T,,,TCGA-CD-5802-01A-11D-1600-08,TCGA-CD-5802-10A-01D-1600-08,,,,,,,,,Somatic,,,,,,,c1b44966-0f72-4c4f-8783-ab3ffe7f17b2,af722e36-4912-45c4-b431-a2ceff596bac,c.479G>A,p.Arg160Lys,p.R160K,ENST00000651961,4/7,78,59,19,110,,,"GSG1,missense_variant,p.R160K,ENST00000651961,NM_001080555.4&NM_001367362.2&NM_001367363.2&NM_001367359.2,c.479G>A,MODERATE,YES,tolerated(0.2),possibly_damaging(0.832),-1;GSG1,missense_variant,p.R124K,ENST00000337630,NM_153823.5&NM_001368007.2,c.371G>A,MODERATE,,tolerated(0.26),benign(0.241),-1;GSG1,missense_variant,p.R124K,ENST00000396302,NM_031289.5,c.371G>A,MODERATE,,tolerated(0.18),possibly_damaging(0.56),-1;GSG1,missense_variant,p.R160K,ENST00000351606,NM_001367364.2&NM_001367360.2&NM_001080554.4&NM_001367358.2&NM_001367361.2,c.479G>A,MODERATE,,tolerated(0.17),possibly_damaging(0.882),-1;GSG1,missense_variant,p.R137K,ENST00000432710,NM_001206842.3,c.410G>A,MODERATE,,tolerated(0.29),probably_damaging(0.995),-1;GSG1,missense_variant,p.R124K,ENST00000457134,NM_001206845.3,c.371G>A,MODERATE,,tolerated(0.27),probably_damaging(0.99),-1;GSG1,missense_variant,p.R147K,ENST00000537302,NM_001206843.3,c.440G>A,MODERATE,,tolerated(0.25),probably_damaging(0.994),-1;GSG1,missense_variant,p.R137K,ENST00000545401,,c.410G>A,MODERATE,,tolerated(0.16),possibly_damaging(0.699),-1;GSG1,missense_variant,p.R184K,ENST00000542415,,c.551G>A,MODERATE,,tolerated(0.23),benign(0.348),-1;GSG1,missense_variant,p.R171K,ENST00000545699,,c.512G>A,MODERATE,,tolerated(0.12),probably_damaging(0.99),-1;FAM234B,intron_variant,,ENST00000537625,,c.970+12721C>T,MODIFIER,,,,1",T,ENSG00000111305,ENST00000651961,Transcript,missense_variant,missense_variant;splice_region_variant,634/2613,479/1089,160/362,R/K,aGa/aAa,COSV60971397,,-1,GSG1,HGNC,HGNC:19716,protein_coding,YES,,ENSP00000498528,,A0A494C0G6.8,UPI0000EE1ABD,,NM_001080555.4;NM_001367362.2;NM_001367363.2;NM_001367359.2,NM_001080555.4,,,tolerated(0.2),possibly_damaging(0.832),4/7,,PANTHER:PTHR10671:SF43;PANTHER:PTHR10671;Pfam:PF07803,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1,,,,,,,,MODERATE,1.0,SNV,,,1,,CACCTCTCTTG,7038f799-3e06-4998-b3c1-69f598faf0b4,836fb985-3ef2-4bd1-9e7c-092e897499f8,0aecac64-5982-4d76-8f31-958f6a00951d,,COSM4040220;COSM4040221;COSM4040222,N,Unknown,,,,muse;mutect2;varscan2
DGKA,1606,BI,GRCh38,chr12,55940719,55940719,+,Silent,SNP,C,C,T,,,TCGA-CD-5802-01A-11D-1600-08,TCGA-CD-5802-10A-01D-1600-08,,,,,,,,,Somatic,,,,,,,c1b44966-0f72-4c4f-8783-ab3ffe7f17b2,af722e36-4912-45c4-b431-a2ceff596bac,c.1014C>T,p.Val338=,p.V338=,ENST00000331886,12/24,436,383,52,145,,,"DGKA,synonymous_variant,p.V338=,ENST00000394147,NM_001351034.1&NM_201444.2&NM_001351040.1&NM_201445.1&NM_001351036.1&NM_201554.1&NM_001351039.1,c.1014C>T,LOW,YES,,,1;DGKA,synonymous_variant,p.V338=,ENST00000331886,NM_001345.5&NM_001351035.1&NM_001351037.1,c.1014C>T,LOW,,,,1;DGKA,synonymous_variant,p.V338=,ENST00000551156,NM_001351033.1&NM_001351038.1,c.1014C>T,LOW,,,,1;DGKA,synonymous_variant,p.V257=,ENST00000555218,,c.771C>T,LOW,,,,1;DGKA,downstream_gene_variant,,ENST00000432422,,,MODIFIER,,,,1;DGKA,downstream_gene_variant,,ENST00000546878,,,MODIFIER,,,,1;DGKA,downstream_gene_variant,,ENST00000547015,,,MODIFIER,,,,1;DGKA,downstream_gene_variant,,ENST00000549368,,,MODIFIER,,,,1;DGKA,downstream_gene_variant,,ENST00000549629,,,MODIFIER,,,,1;DGKA,downstream_gene_variant,,ENST00000551707,,,MODIFIER,,,,1;DGKA,upstream_gene_variant,,ENST00000552903,,,MODIFIER,,,,1;DGKA,downstream_gene_variant,,ENST00000553783,,,MODIFIER,,,,1;DGKA,downstream_gene_variant,,ENST00000555025,,,MODIFIER,,,,1;DGKA,downstream_gene_variant,,ENST00000555090,,,MODIFIER,,,,1;DGKA,downstream_gene_variant,,ENST00000556001,,,MODIFIER,,,,1;DGKA,downstream_gene_variant,,ENST00000557080,,,MODIFIER,,,,1;DGKA,non_coding_transcript_exon_variant,,ENST00000549079,,n.740C>T,MODIFIER,,,,1;DGKA,downstream_gene_variant,,ENST00000549323,,,MODIFIER,,,,1;DGKA,3_prime_UTR_variant,,ENST00000402956,,c.*181C>T,MODIFIER,,,,1;DGKA,3_prime_UTR_variant,,ENST00000553084,,c.*668C>T,MODIFIER,,,,1;DGKA,3_prime_UTR_variant,,ENST00000557180,,c.*128C>T,MODIFIER,,,,1;DGKA,non_coding_transcript_exon_variant,,ENST00000552478,,n.2828C>T,MODIFIER,,,,1;DGKA,non_coding_transcript_exon_variant,,ENST00000551739,,n.1966C>T,MODIFIER,,,,1;DGKA,non_coding_transcript_exon_variant,,ENST00000551296,,n.2629C>T,MODIFIER,,,,1;DGKA,non_coding_transcript_exon_variant,,ENST00000548047,,n.1144C>T,MODIFIER,,,,1;DGKA,non_coding_transcript_exon_variant,,ENST00000547358,,n.1141C>T,MODIFIER,,,,1;DGKA,non_coding_transcript_exon_variant,,ENST00000552652,,n.681C>T,MODIFIER,,,,1;DGKA,non_coding_transcript_exon_variant,,ENST00000554434,,n.588C>T,MODIFIER,,,,1;DGKA,downstream_gene_variant,,ENST00000546895,,,MODIFIER,,,,1;DGKA,downstream_gene_variant,,ENST00000546995,,,MODIFIER,,,,1;DGKA,downstream_gene_variant,,ENST00000547324,,,MODIFIER,,,,1;DGKA,downstream_gene_variant,,ENST00000547535,,,MODIFIER,,,,1;DGKA,downstream_gene_variant,,ENST00000548407,,,MODIFIER,,,,1;DGKA,downstream_gene_variant,,ENST00000548479,,,MODIFIER,,,,1;DGKA,downstream_gene_variant,,ENST00000548549,,,MODIFIER,,,,1;DGKA,downstream_gene_variant,,ENST00000549085,,,MODIFIER,,,,1;DGKA,downstream_gene_variant,,ENST00000549097,,,MODIFIER,,,,1;DGKA,downstream_gene_variant,,ENST00000549986,,,MODIFIER,,,,1;DGKA,downstream_gene_variant,,ENST00000550484,,,MODIFIER,,,,1;DGKA,downstream_gene_variant,,ENST00000550888,,,MODIFIER,,,,1;DGKA,upstream_gene_variant,,ENST00000551585,,,MODIFIER,,,,1;DGKA,downstream_gene_variant,,ENST00000551615,,,MODIFIER,,,,1;DGKA,downstream_gene_variant,,ENST00000552335,,,MODIFIER,,,,1;DGKA,downstream_gene_variant,,ENST00000552687,,,MODIFIER,,,,1;DGKA,downstream_gene_variant,,ENST00000556344,,,MODIFIER,,,,1",T,ENSG00000065357,ENST00000331886,Transcript,synonymous_variant,synonymous_variant,1278/2727,1014/2208,338/735,V,gtC/gtT,COSV59385979,,1,DGKA,HGNC,HGNC:2849,protein_coding,,CCDS8896.1,ENSP00000328405,P23743.202,A0A024RB23.54,UPI000007417B,P23743-1,NM_001345.5;NM_001351035.1;NM_001351037.1,NM_001345.5,P1,,,,12/24,,PANTHER:PTHR11255;PANTHER:PTHR11255:SF38,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1,,,,,,,,LOW,,SNV,5.0,,1,,AGTGTCCTGGT,7038f799-3e06-4998-b3c1-69f598faf0b4,836fb985-3ef2-4bd1-9e7c-092e897499f8,0aecac64-5982-4d76-8f31-958f6a00951d,,COSM4043398,N,Unknown,,,,muse;mutect2;varscan2
DGKA,1606,BI,GRCh38,chr12,55941575,55941575,+,Missense_Mutation,SNP,C,C,T,,,TCGA-CD-5802-01A-11D-1600-08,TCGA-CD-5802-10A-01D-1600-08,,,,,,,,,Somatic,,,,,,,c1b44966-0f72-4c4f-8783-ab3ffe7f17b2,af722e36-4912-45c4-b431-a2ceff596bac,c.1241C>T,p.Pro414Leu,p.P414L,ENST00000331886,15/24,952,876,76,260,,,"DGKA,missense_variant,p.P414L,ENST00000394147,NM_001351034.1&NM_201444.2&NM_001351040.1&NM_201445.1&NM_001351036.1&NM_201554.1&NM_001351039.1,c.1241C>T,MODERATE,YES,deleterious(0.01),probably_damaging(0.98),1;DGKA,missense_variant,p.P414L,ENST00000331886,NM_001345.5&NM_001351035.1&NM_001351037.1,c.1241C>T,MODERATE,,deleterious(0.01),probably_damaging(0.98),1;DGKA,missense_variant,p.P414L,ENST00000551156,NM_001351033.1&NM_001351038.1,c.1241C>T,MODERATE,,deleterious(0.01),probably_damaging(0.98),1;DGKA,missense_variant,p.P333L,ENST00000555218,,c.998C>T,MODERATE,,deleterious(0),probably_damaging(1),1;DGKA,intron_variant,,ENST00000552903,,c.80+250C>T,MODIFIER,,,,1;DGKA,downstream_gene_variant,,ENST00000432422,,,MODIFIER,,,,1;DGKA,downstream_gene_variant,,ENST00000546878,,,MODIFIER,,,,1;DGKA,downstream_gene_variant,,ENST00000549368,,,MODIFIER,,,,1;DGKA,downstream_gene_variant,,ENST00000549629,,,MODIFIER,,,,1;DGKA,downstream_gene_variant,,ENST00000551707,,,MODIFIER,,,,1;DGKA,downstream_gene_variant,,ENST00000553783,,,MODIFIER,,,,1;DGKA,downstream_gene_variant,,ENST00000555025,,,MODIFIER,,,,1;DGKA,downstream_gene_variant,,ENST00000555090,,,MODIFIER,,,,1;DGKA,downstream_gene_variant,,ENST00000556001,,,MODIFIER,,,,1;DGKA,downstream_gene_variant,,ENST00000557080,,,MODIFIER,,,,1;DGKA,non_coding_transcript_exon_variant,,ENST00000549079,,n.967C>T,MODIFIER,,,,1;DGKA,downstream_gene_variant,,ENST00000549323,,,MODIFIER,,,,1;DGKA,3_prime_UTR_variant,,ENST00000402956,,c.*408C>T,MODIFIER,,,,1;DGKA,3_prime_UTR_variant,,ENST00000553084,,c.*895C>T,MODIFIER,,,,1;DGKA,3_prime_UTR_variant,,ENST00000557180,,c.*355C>T,MODIFIER,,,,1;DGKA,non_coding_transcript_exon_variant,,ENST00000552478,,n.3326C>T,MODIFIER,,,,1;DGKA,non_coding_transcript_exon_variant,,ENST00000551739,,n.2193C>T,MODIFIER,,,,1;DGKA,non_coding_transcript_exon_variant,,ENST00000551296,,n.2856C>T,MODIFIER,,,,1;DGKA,non_coding_transcript_exon_variant,,ENST00000548047,,n.1371C>T,MODIFIER,,,,1;DGKA,non_coding_transcript_exon_variant,,ENST00000551585,,n.107C>T,MODIFIER,,,,1;DGKA,downstream_gene_variant,,ENST00000546895,,,MODIFIER,,,,1;DGKA,downstream_gene_variant,,ENST00000546995,,,MODIFIER,,,,1;DGKA,downstream_gene_variant,,ENST00000547324,,,MODIFIER,,,,1;DGKA,downstream_gene_variant,,ENST00000547358,,,MODIFIER,,,,1;DGKA,downstream_gene_variant,,ENST00000547535,,,MODIFIER,,,,1;DGKA,downstream_gene_variant,,ENST00000548407,,,MODIFIER,,,,1;DGKA,downstream_gene_variant,,ENST00000548479,,,MODIFIER,,,,1;DGKA,downstream_gene_variant,,ENST00000548549,,,MODIFIER,,,,1;DGKA,downstream_gene_variant,,ENST00000549085,,,MODIFIER,,,,1;DGKA,downstream_gene_variant,,ENST00000549097,,,MODIFIER,,,,1;DGKA,downstream_gene_variant,,ENST00000549986,,,MODIFIER,,,,1;DGKA,downstream_gene_variant,,ENST00000550484,,,MODIFIER,,,,1;DGKA,downstream_gene_variant,,ENST00000550888,,,MODIFIER,,,,1;DGKA,downstream_gene_variant,,ENST00000551615,,,MODIFIER,,,,1;DGKA,downstream_gene_variant,,ENST00000552335,,,MODIFIER,,,,1;DGKA,downstream_gene_variant,,ENST00000552652,,,MODIFIER,,,,1;DGKA,downstream_gene_variant,,ENST00000552687,,,MODIFIER,,,,1;DGKA,downstream_gene_variant,,ENST00000554434,,,MODIFIER,,,,1;DGKA,downstream_gene_variant,,ENST00000556344,,,MODIFIER,,,,1",T,ENSG00000065357,ENST00000331886,Transcript,missense_variant,missense_variant,1505/2727,1241/2208,414/735,P/L,cCt/cTt,COSV59385989,,1,DGKA,HGNC,HGNC:2849,protein_coding,,CCDS8896.1,ENSP00000328405,P23743.202,A0A024RB23.54,UPI000007417B,P23743-1,NM_001345.5;NM_001351035.1;NM_001351037.1,NM_001345.5,P1,,deleterious(0.01),probably_damaging(0.98),15/24,,PROSITE_profiles:PS50146;PANTHER:PTHR11255;PANTHER:PTHR11255:SF38;Pfam:PF00781;Gene3D:3.40.50.10330;SMART:SM00046;Superfamily:SSF111331,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1,,,,,,,,MODERATE,,SNV,5.0,,1,,TGGTCCTGAGA,7038f799-3e06-4998-b3c1-69f598faf0b4,836fb985-3ef2-4bd1-9e7c-092e897499f8,0aecac64-5982-4d76-8f31-958f6a00951d,,COSM4043400,N,Unknown,,,,muse;mutect2
SUOX,6821,BI,GRCh38,chr12,56003968,56003968,+,Silent,SNP,C,C,T,,,TCGA-CD-5802-01A-11D-1600-08,TCGA-CD-5802-10A-01D-1600-08,,,,,,,,,Somatic,,,,,,,c1b44966-0f72-4c4f-8783-ab3ffe7f17b2,af722e36-4912-45c4-b431-a2ceff596bac,c.579C>T,p.Pro193=,p.P193=,ENST00000266971,5/5,434,415,18,92,,,"SUOX,synonymous_variant,p.P193=,ENST00000394109,,c.579C>T,LOW,YES,,,1;SUOX,synonymous_variant,p.P193=,ENST00000394115,NM_000456.3,c.579C>T,LOW,,,,1;SUOX,synonymous_variant,p.P193=,ENST00000548274,,c.579C>T,LOW,,,,1;SUOX,synonymous_variant,p.P193=,ENST00000266971,NM_001032386.2,c.579C>T,LOW,,,,1;SUOX,synonymous_variant,p.P193=,ENST00000356124,NM_001032387.2,c.579C>T,LOW,,,,1;SUOX,intron_variant,,ENST00000551841,,c.268-186C>T,MODIFIER,,,,1;IKZF4,upstream_gene_variant,,ENST00000262032,NM_001351089.2,,MODIFIER,,,,1;SUOX,downstream_gene_variant,,ENST00000546833,,,MODIFIER,,,,1;SUOX,downstream_gene_variant,,ENST00000547586,,,MODIFIER,,,,1;SUOX,downstream_gene_variant,,ENST00000552258,,,MODIFIER,,,,1;SUOX,non_coding_transcript_exon_variant,,ENST00000550340,,n.464C>T,MODIFIER,,,,1;IKZF4,upstream_gene_variant,,ENST00000548601,,,MODIFIER,,,,1;SUOX,downstream_gene_variant,,ENST00000550121,,,MODIFIER,,,,1;SUOX,downstream_gene_variant,,ENST00000550478,,,MODIFIER,,,,1;SUOX,downstream_gene_variant,,ENST00000551698,,,MODIFIER,,,,1;SUOX,downstream_gene_variant,,ENST00000552363,,,MODIFIER,,,,1;SUOX,synonymous_variant,p.P193=,ENST00000550065,,c.579C>T,LOW,,,,1;SUOX,downstream_gene_variant,,ENST00000546712,,,MODIFIER,,,,1;SUOX,downstream_gene_variant,,ENST00000552813,,,MODIFIER,,,,1",T,ENSG00000139531,ENST00000266971,Transcript,synonymous_variant,synonymous_variant,762/2319,579/1638,193/545,P,ccC/ccT,COSV56268227,,1,SUOX,HGNC,HGNC:11460,protein_coding,,CCDS8901.2,ENSP00000266971,P51687.201,A0A024RB79.54,UPI00001FC4A1,,NM_001032386.2,NM_001032386.2,P1,,,,5/5,,Gene3D:3.90.420.10;Prints:PR00407;PANTHER:PTHR19372;PANTHER:PTHR19372:SF7;Superfamily:SSF56524;CDD:cd02111,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1,,,,,,,,LOW,,SNV,2.0,,1,1.0,CGGCCCTTTAA,7038f799-3e06-4998-b3c1-69f598faf0b4,836fb985-3ef2-4bd1-9e7c-092e897499f8,0aecac64-5982-4d76-8f31-958f6a00951d,,COSM4043415,N,Unknown,,,,muse;mutect2
MYCBP2,23077,BI,GRCh38,chr13,77097704,77097704,+,Missense_Mutation,SNP,C,C,T,rs1261027973,,TCGA-CD-5802-01A-11D-1600-08,TCGA-CD-5802-10A-01D-1600-08,,,,,,,,,Somatic,,,,,,,c1b44966-0f72-4c4f-8783-ab3ffe7f17b2,af722e36-4912-45c4-b431-a2ceff596bac,c.9336G>A,p.Met3112Ile,p.M3112I,ENST00000357337,57/84,265,218,47,274,,,"MYCBP2,missense_variant,p.M3150I,ENST00000544440,NM_015057.5,c.9450G>A,MODERATE,YES,tolerated(0.16),benign(0),-1;MYCBP2,missense_variant,p.M3112I,ENST00000357337,,c.9336G>A,MODERATE,,tolerated(0.15),benign(0),-1;AC001226.2,intron_variant,,ENST00000638101,,c.170-221C>T,MODIFIER,,,,1;MYCBP2,downstream_gene_variant,,ENST00000462987,,,MODIFIER,,,,-1;MYCBP2,downstream_gene_variant,,ENST00000482517,,,MODIFIER,,,,-1;MYCBP2,upstream_gene_variant,,ENST00000485061,,,MODIFIER,,,,-1;MYCBP2,downstream_gene_variant,,ENST00000498073,,,MODIFIER,,,,-1;AC001226.2,intron_variant,,ENST00000637192,,c.214-11944C>T,MODIFIER,,,,1;MYCBP2-AS1,intron_variant,,ENST00000593933,,n.100-221C>T,MODIFIER,,,,1;MYCBP2-AS1,intron_variant,,ENST00000627409,,n.31+20771C>T,MODIFIER,,,,1;MYCBP2-AS1,intron_variant,,ENST00000629771,,n.129-221C>T,MODIFIER,,,,1",T,ENSG00000005810,ENST00000357337,Transcript,missense_variant,missense_variant,9429/14736,9336/13923,3112/4640,M/I,atG/atA,rs1261027973;COSV62018187,,-1,MYCBP2,HGNC,HGNC:23386,protein_coding,,,ENSP00000349892,,A0A499FJI4.5,UPI0000212757,,,,A2,,tolerated(0.15),benign(0),57/84,,PANTHER:PTHR45943;PANTHER:PTHR45943:SF1,,,,,,,,,,,,,,,,,,,,6.765079888282344e-06,0.0,0.0,6.64452018099837e-05,0.0,0.0,0.0,0.0,0.0,0.0,0.0,,,,0;1,,,,,,,,MODERATE,,SNV,1.0,,0;1,,GACTTCATTGT,7038f799-3e06-4998-b3c1-69f598faf0b4,836fb985-3ef2-4bd1-9e7c-092e897499f8,0aecac64-5982-4d76-8f31-958f6a00951d,,COSM4048451;COSM4048452;COSM4048453,N,Unknown,,,,muse;mutect2;varscan2
FANCM,57697,BI,GRCh38,chr14,45187806,45187806,+,Missense_Mutation,SNP,G,G,A,,,TCGA-CD-5802-01A-11D-1600-08,TCGA-CD-5802-10A-01D-1600-08,,,,,,,,,Somatic,,,,,,,c1b44966-0f72-4c4f-8783-ab3ffe7f17b2,af722e36-4912-45c4-b431-a2ceff596bac,c.4698G>A,p.Met1566Ile,p.M1566I,ENST00000267430,19/23,65,50,15,84,,,"FANCM,missense_variant,p.M1566I,ENST00000267430,NM_020937.4,c.4698G>A,MODERATE,YES,tolerated(0.07),benign(0.034),1;FANCM,missense_variant,p.M1540I,ENST00000542564,NM_001308133.2,c.4620G>A,MODERATE,,tolerated(0.07),benign(0.034),1;FANCM,missense_variant,p.M1082I,ENST00000556250,,c.3246G>A,MODERATE,,tolerated(0.07),benign(0.086),1;FANCM,missense_variant,p.M499I,ENST00000554809,,c.1497G>A,MODERATE,,tolerated(0.07),benign(0.049),1;FANCM,non_coding_transcript_exon_variant,,ENST00000555013,,n.531G>A,MODIFIER,,,,1",A,ENSG00000187790,ENST00000267430,Transcript,missense_variant,missense_variant,4800/7131,4698/6147,1566/2048,M/I,atG/atA,COSV57500929,,1,FANCM,HGNC,HGNC:23168,protein_coding,YES,CCDS32070.1,ENSP00000267430,Q8IYD8.162,,UPI000059F032,Q8IYD8-1,NM_020937.4,NM_020937.4,P1,,tolerated(0.07),benign(0.034),19/23,,PANTHER:PTHR14074;PANTHER:PTHR14074:SF33,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1,,,,,,,,MODERATE,1.0,SNV,1.0,,1,1.0,TACATGAAATC,7038f799-3e06-4998-b3c1-69f598faf0b4,836fb985-3ef2-4bd1-9e7c-092e897499f8,0aecac64-5982-4d76-8f31-958f6a00951d,,COSM4050909,N,Unknown,,,,muse;mutect2;varscan2
ZFYVE26,23503,BI,GRCh38,chr14,67783326,67783326,+,Missense_Mutation,SNP,G,G,A,,,TCGA-CD-5802-01A-11D-1600-08,TCGA-CD-5802-10A-01D-1600-08,,,,,,,,,Somatic,,,,,,,c1b44966-0f72-4c4f-8783-ab3ffe7f17b2,af722e36-4912-45c4-b431-a2ceff596bac,c.3826C>T,p.Pro1276Ser,p.P1276S,ENST00000347230,21/42,248,198,49,309,,,"ZFYVE26,missense_variant,p.P1276S,ENST00000678386,,c.3826C>T,MODERATE,YES,tolerated(0.81),benign(0.005),-1;ZFYVE26,missense_variant,p.P1276S,ENST00000676512,,c.3826C>T,MODERATE,,tolerated(0.81),benign(0.005),-1;ZFYVE26,missense_variant,p.P1276S,ENST00000347230,NM_015346.4,c.3826C>T,MODERATE,,tolerated(0.83),benign(0.007),-1;ZFYVE26,missense_variant,p.P1276S,ENST00000676620,,c.3826C>T,MODERATE,,tolerated(0.81),benign(0.005),-1;ZFYVE26,missense_variant,p.P1276S,ENST00000555452,,c.3826C>T,MODERATE,,tolerated(0.51),benign(0.023),-1;ZFYVE26,3_prime_UTR_variant,,ENST00000554557,,c.*2123C>T,MODIFIER,,,,-1;ZFYVE26,non_coding_transcript_exon_variant,,ENST00000554523,,n.3963C>T,MODIFIER,,,,-1;ZFYVE26,upstream_gene_variant,,ENST00000557204,,,MODIFIER,,,,-1",A,ENSG00000072121,ENST00000347230,Transcript,missense_variant,missense_variant,3966/9674,3826/7620,1276/2539,P/S,Ccg/Tcg,COSV61328174,,-1,ZFYVE26,HGNC,HGNC:20761,protein_coding,,CCDS9788.1,ENSP00000251119,Q68DK2.135,,UPI00001FD735,,NM_015346.4,NM_015346.4,P2,,tolerated(0.83),benign(0.007),21/42,,PANTHER:PTHR46591;MobiDB_lite:mobidb-lite,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1,,,,,,,,MODERATE,,SNV,1.0,,1,1.0,CCTCGGGGAGC,7038f799-3e06-4998-b3c1-69f598faf0b4,836fb985-3ef2-4bd1-9e7c-092e897499f8,0aecac64-5982-4d76-8f31-958f6a00951d,,COSM4051979,N,Unknown,,,,muse;mutect2;varscan2
MAPKBP1,23005,BI,GRCh38,chr15,41823598,41823598,+,Silent,SNP,C,C,A,,,TCGA-CD-5802-01A-11D-1600-08,TCGA-CD-5802-10A-01D-1600-08,,,,,,,,,Somatic,,,,,,,c1b44966-0f72-4c4f-8783-ab3ffe7f17b2,af722e36-4912-45c4-b431-a2ceff596bac,c.3768C>A,p.Ala1256=,p.A1256=,ENST00000456763,30/32,74,59,14,100,,,"MAPKBP1,synonymous_variant,p.A1250=,ENST00000457542,NM_014994.3,c.3750C>A,LOW,,,,1;MAPKBP1,synonymous_variant,p.A1256=,ENST00000456763,NM_001128608.2,c.3768C>A,LOW,YES,,,1;MAPKBP1,intron_variant,,ENST00000514566,NM_001265611.2,c.3382+592C>A,MODIFIER,,,,1;JMJD7-PLA2G4B,upstream_gene_variant,,ENST00000342159,NM_001198588.1,,MODIFIER,,,,1;JMJD7-PLA2G4B,upstream_gene_variant,,ENST00000382448,NM_005090.3,,MODIFIER,YES,,,1;JMJD7,upstream_gene_variant,,ENST00000397299,NM_001114632.2,,MODIFIER,YES,,,1;JMJD7,upstream_gene_variant,,ENST00000408047,,,MODIFIER,,,,1;JMJD7,upstream_gene_variant,,ENST00000431823,,,MODIFIER,,,,1;JMJD7,upstream_gene_variant,,ENST00000405106,,,MODIFIER,,,,1;MAPKBP1,3_prime_UTR_variant,,ENST00000512970,,c.*2564C>A,MODIFIER,,,,1;MAPKBP1,3_prime_UTR_variant,,ENST00000505373,,c.*3301C>A,MODIFIER,,,,1;MAPKBP1,non_coding_transcript_exon_variant,,ENST00000505061,,n.4413C>A,MODIFIER,,,,1;JMJD7-PLA2G4B,upstream_gene_variant,,ENST00000490848,,,MODIFIER,,,,1;JMJD7-PLA2G4B,upstream_gene_variant,,ENST00000491746,,,MODIFIER,,,,1;MAPKBP1,downstream_gene_variant,,ENST00000502695,,,MODIFIER,,,,1;MAPKBP1,downstream_gene_variant,,ENST00000506301,,,MODIFIER,,,,1;MAPKBP1,downstream_gene_variant,,ENST00000508050,,,MODIFIER,,,,1;MAPKBP1,downstream_gene_variant,,ENST00000512433,,,MODIFIER,,,,1;AC020659.2,downstream_gene_variant,,ENST00000510176,,,MODIFIER,YES,,,-1;AC020659.2,downstream_gene_variant,,ENST00000512295,,,MODIFIER,,,,-1",A,ENSG00000137802,ENST00000456763,Transcript,synonymous_variant,synonymous_variant,3964/7158,3768/4545,1256/1514,A,gcC/gcA,COSV52961230,,1,MAPKBP1,HGNC,HGNC:29536,protein_coding,YES,CCDS45239.1,ENSP00000393099,O60336.158,,UPI00002375CB,O60336-1,NM_001128608.2,,A2,,,,30/32,,PANTHER:PTHR45589;PANTHER:PTHR45589:SF5;MobiDB_lite:mobidb-lite,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1,,,,,,,,LOW,1.0,SNV,1.0,,1,1.0,ATGGCCAAGAT,7038f799-3e06-4998-b3c1-69f598faf0b4,836fb985-3ef2-4bd1-9e7c-092e897499f8,0aecac64-5982-4d76-8f31-958f6a00951d,,COSM4054601;COSM4054602,N,Unknown,,,,muse;mutect2;varscan2
NCBP3,55421,BI,GRCh38,chr17,3813139,3813139,+,Nonsense_Mutation,SNP,G,G,A,novel,,TCGA-CD-5802-01A-11D-1600-08,TCGA-CD-5802-10A-01D-1600-08,,,,,,,,,Somatic,,,,,,,c1b44966-0f72-4c4f-8783-ab3ffe7f17b2,af722e36-4912-45c4-b431-a2ceff596bac,c.1768C>T,p.Gln590Ter,p.Q590*,ENST00000389005,13/13,227,190,37,266,,,"NCBP3,stop_gained,p.Q590*,ENST00000389005,NM_001114118.3,c.1768C>T,HIGH,YES,,,-1;NCBP3,stop_gained,p.Q38*,ENST00000576523,,c.112C>T,HIGH,,,,-1;NCBP3,3_prime_UTR_variant,,ENST00000574911,,c.*976C>T,MODIFIER,,,,-1;NCBP3,non_coding_transcript_exon_variant,,ENST00000575815,,n.2485C>T,MODIFIER,,,,-1",A,ENSG00000074356,ENST00000389005,Transcript,stop_gained,stop_gained,1791/12772,1768/1863,590/620,Q/*,Cag/Tag,,,-1,NCBP3,HGNC,HGNC:24612,protein_coding,YES,CCDS45578.1,ENSP00000373657,Q53F19.121,,UPI00004DDA14,Q53F19-1,NM_001114118.3,NM_001114118.3,P1,,,,13/13,,MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,HIGH,1.0,SNV,5.0,,,,AGACTGCTCTT,7038f799-3e06-4998-b3c1-69f598faf0b4,836fb985-3ef2-4bd1-9e7c-092e897499f8,0aecac64-5982-4d76-8f31-958f6a00951d,,,N,Unknown,,,,muse;mutect2;varscan2
NCBP3,55421,BI,GRCh38,chr17,3813140,3813140,+,Silent,SNP,C,C,T,,,TCGA-CD-5802-01A-11D-1600-08,TCGA-CD-5802-10A-01D-1600-08,,,,,,,,,Somatic,,,,,,,c1b44966-0f72-4c4f-8783-ab3ffe7f17b2,af722e36-4912-45c4-b431-a2ceff596bac,c.1767G>A,p.Glu589=,p.E589=,ENST00000389005,13/13,222,185,36,260,,,"NCBP3,synonymous_variant,p.E589=,ENST00000389005,NM_001114118.3,c.1767G>A,LOW,YES,,,-1;NCBP3,synonymous_variant,p.E37=,ENST00000576523,,c.111G>A,LOW,,,,-1;NCBP3,3_prime_UTR_variant,,ENST00000574911,,c.*975G>A,MODIFIER,,,,-1;NCBP3,non_coding_transcript_exon_variant,,ENST00000575815,,n.2484G>A,MODIFIER,,,,-1",T,ENSG00000074356,ENST00000389005,Transcript,synonymous_variant,synonymous_variant,1790/12772,1767/1863,589/620,E,gaG/gaA,COSV99339671,,-1,NCBP3,HGNC,HGNC:24612,protein_coding,YES,CCDS45578.1,ENSP00000373657,Q53F19.121,,UPI00004DDA14,Q53F19-1,NM_001114118.3,NM_001114118.3,P1,,,,13/13,,MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1,,,,,,,,LOW,1.0,SNV,5.0,,1,,GACTGCTCTTT,7038f799-3e06-4998-b3c1-69f598faf0b4,836fb985-3ef2-4bd1-9e7c-092e897499f8,0aecac64-5982-4d76-8f31-958f6a00951d,,,N,Unknown,,,,muse;mutect2;varscan2
RHBDL3,162494,BI,GRCh38,chr17,32288898,32288898,+,Missense_Mutation,SNP,G,G,A,rs776334303,,TCGA-CD-5802-01A-11D-1600-08,TCGA-CD-5802-10A-01D-1600-08,,,,,,,,,Somatic,,,,,,,c1b44966-0f72-4c4f-8783-ab3ffe7f17b2,af722e36-4912-45c4-b431-a2ceff596bac,c.401G>A,p.Arg134Gln,p.R134Q,ENST00000269051,4/9,56,44,12,67,,,"RHBDL3,missense_variant,p.R134Q,ENST00000269051,NM_138328.3,c.401G>A,MODERATE,,deleterious(0),probably_damaging(0.99),1;RHBDL3,missense_variant,p.R36Q,ENST00000536287,NM_001363836.1,c.107G>A,MODERATE,,deleterious(0),probably_damaging(0.99),1;RHBDL3,missense_variant,p.R126Q,ENST00000538145,NM_001330181.2&NM_001363834.1,c.377G>A,MODERATE,,deleterious(0.01),probably_damaging(0.99),1;RHBDL3,missense_variant,p.R134Q,ENST00000431505,NM_001363835.1,c.401G>A,MODERATE,YES,deleterious(0.02),probably_damaging(0.922),1;RHBDL3,3_prime_UTR_variant,,ENST00000578006,,c.*224G>A,MODIFIER,,,,1;RHBDL3,non_coding_transcript_exon_variant,,ENST00000582967,,n.773G>A,MODIFIER,,,,1",A,ENSG00000141314,ENST00000269051,Transcript,missense_variant,missense_variant,759/5003,401/1215,134/404,R/Q,cGa/cAa,rs776334303;COSV52186052;COSV52188520,,1,RHBDL3,HGNC,HGNC:16502,protein_coding,,CCDS32613.1,ENSP00000269051,P58872.151,,UPI0000133858,P58872-1,NM_138328.3,NM_138328.3,P1,,deleterious(0),probably_damaging(0.99),4/9,,PIRSF:PIRSF037470;PANTHER:PTHR45840;PANTHER:PTHR45840:SF5,,,,,,,,,1.591e-05,0.0,2.891e-05,0.0,0.0,9.239e-05,0.0,0.0,3.266e-05,9.239e-05,gnomAD_FIN,1.3519699677999595e-05,2.4310800654347983e-05,0.0,0.0,0.0,0.0,9.41973994486034e-05,0.0,0.0,0.0,0.0,,,,0;1;1,,,,,,,,MODERATE,,SNV,1.0,,0;1;1,,GCAGCGACTTA,7038f799-3e06-4998-b3c1-69f598faf0b4,836fb985-3ef2-4bd1-9e7c-092e897499f8,0aecac64-5982-4d76-8f31-958f6a00951d,,COSM4065399,N,Unknown,,,,muse;mutect2;varscan2
EFTUD2,9343,BI,GRCh38,chr17,44862847,44862847,+,Silent,SNP,G,G,A,rs149288120,,TCGA-CD-5802-01A-11D-1600-08,TCGA-CD-5802-10A-01D-1600-08,,,,,,,,,Somatic,,,,,,,c1b44966-0f72-4c4f-8783-ab3ffe7f17b2,af722e36-4912-45c4-b431-a2ceff596bac,c.1473C>T,p.His491=,p.H491=,ENST00000426333,16/28,111,79,32,111,,,"EFTUD2,synonymous_variant,p.H491=,ENST00000426333,NM_004247.4,c.1473C>T,LOW,YES,,,-1;EFTUD2,synonymous_variant,p.H491=,ENST00000591382,NM_001258353.1,c.1473C>T,LOW,,,,-1;EFTUD2,synonymous_variant,p.H481=,ENST00000592576,NM_001258354.1,c.1443C>T,LOW,,,,-1;EFTUD2,synonymous_variant,p.H456=,ENST00000402521,NM_001142605.1,c.1368C>T,LOW,,,,-1;EFTUD2,non_coding_transcript_exon_variant,,ENST00000585616,,n.351C>T,MODIFIER,,,,-1;EFTUD2,non_coding_transcript_exon_variant,,ENST00000586276,,n.749C>T,MODIFIER,,,,-1;EFTUD2,non_coding_transcript_exon_variant,,ENST00000590367,,n.1201C>T,MODIFIER,,,,-1;EFTUD2,non_coding_transcript_exon_variant,,ENST00000586654,,n.528C>T,MODIFIER,,,,-1;EFTUD2,non_coding_transcript_exon_variant,,ENST00000585794,,n.491C>T,MODIFIER,,,,-1;EFTUD2,non_coding_transcript_exon_variant,,ENST00000587914,,n.468C>T,MODIFIER,,,,-1;EFTUD2,upstream_gene_variant,,ENST00000590977,,,MODIFIER,,,,-1;EFTUD2,downstream_gene_variant,,ENST00000591856,,,MODIFIER,,,,-1",A,ENSG00000108883,ENST00000426333,Transcript,synonymous_variant,synonymous_variant,1554/4326,1473/2919,491/972,H,caC/caT,rs149288120,,-1,EFTUD2,HGNC,HGNC:30858,protein_coding,YES,CCDS11489.1,ENSP00000392094,Q15029.224,,UPI0000137931,Q15029-1,NM_004247.4,NM_004247.4,P1,,,,16/28,,Gene3D:2.40.30.10;PDB-ENSP_mappings:3jcr.B;PDB-ENSP_mappings:5mqf.B;PDB-ENSP_mappings:5o9z.B;PDB-ENSP_mappings:5xjc.C;PDB-ENSP_mappings:5yzg.C;PDB-ENSP_mappings:5z56.C;PDB-ENSP_mappings:5z57.C;PDB-ENSP_mappings:5z58.C;PDB-ENSP_mappings:6ah0.C;PDB-ENSP_mappings:6ahd.C;PDB-ENSP_mappings:6ff4.B;PDB-ENSP_mappings:6ff7.B;PDB-ENSP_mappings:6icz.C;PDB-ENSP_mappings:6id0.C;PDB-ENSP_mappings:6id1.C;PDB-ENSP_mappings:6qdv.C;PDB-ENSP_mappings:6qw6.5C;PDB-ENSP_mappings:6qx9.5C;Pfam:PF03144;PANTHER:PTHR42908;PANTHER:PTHR42908:SF6;Superfamily:SSF50447;CDD:cd04090,,,,,,,0.0004539,0.0,3.98e-05,0.000123,0.0001157,0.0,0.0001087,0.0,1.761e-05,0.0,0.0,0.0004539,AA,3.379569898243062e-05,4.862869900534861e-05,0.0,0.0,0.0,0.0,0.0,0.0,4.629629984265193e-05,0.0,0.0,4.862869900534861e-05,afr,,,,,,,,,,LOW,1.0,SNV,1.0,,,1.0,AAGGCGTGAAA,7038f799-3e06-4998-b3c1-69f598faf0b4,836fb985-3ef2-4bd1-9e7c-092e897499f8,0aecac64-5982-4d76-8f31-958f6a00951d,,COSM4066985,N,Unknown,,,,muse;mutect2;varscan2
ABCA9,10350,BI,GRCh38,chr17,69008166,69008176,+,Frame_Shift_Del,DEL,CCAGTGCTTGG,CCAGTGCTTGG,-,novel,,TCGA-CD-5802-01A-11D-1600-08,TCGA-CD-5802-10A-01D-1600-08,,,,,,,,,Somatic,,,,,,,c1b44966-0f72-4c4f-8783-ab3ffe7f17b2,af722e36-4912-45c4-b431-a2ceff596bac,c.3207_3217del,p.Gln1070GlyfsTer20,p.Q1070Gfs*20,ENST00000340001,24/39,259,223,36,264,,,"ABCA9,frameshift_variant,p.Q1070Gfs*20,ENST00000340001,NM_080283.4,c.3207_3217del,HIGH,YES,,,-1;ABCA9,frameshift_variant,p.Q1070Gfs*20,ENST00000453985,,c.3207_3217del,HIGH,,,,-1;ABCA9,downstream_gene_variant,,ENST00000492580,,,MODIFIER,,,,-1;ABCA9-AS1,intron_variant,,ENST00000458677,,n.80+3376_80+3386del,MODIFIER,,,,1;ABCA9-AS1,intron_variant,,ENST00000630625,,n.378-3814_378-3804del,MODIFIER,,,,1;ABCA9-AS1,upstream_gene_variant,,ENST00000627453,,,MODIFIER,,,,1;ABCA9-AS1,upstream_gene_variant,,ENST00000627596,,,MODIFIER,,,,1;ABCA9-AS1,upstream_gene_variant,,ENST00000627957,,,MODIFIER,,,,1;ABCA9-AS1,upstream_gene_variant,,ENST00000630575,,,MODIFIER,,,,1",-,ENSG00000154258,ENST00000340001,Transcript,frameshift_variant,frameshift_variant,3282-3292/6377,3207-3217/4875,1069-1073/1624,GQALV/GX,ggCCAAGCACTGGtg/ggtg,,,-1,ABCA9,HGNC,HGNC:39,protein_coding,YES,CCDS11681.1,ENSP00000342216,Q8IUA7.135,,UPI00000747B1,Q8IUA7-1,NM_080283.4,NM_080283.4,P1,,,,24/39,,Pfam:PF12698;PANTHER:PTHR19229;PANTHER:PTHR19229:SF120;Transmembrane_helices:TMhelix,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,HIGH,1.0,deletion,1.0,,,,CATCCACCAGTGCTTGGCCAAA,7038f799-3e06-4998-b3c1-69f598faf0b4,836fb985-3ef2-4bd1-9e7c-092e897499f8,0aecac64-5982-4d76-8f31-958f6a00951d,,,N,Unknown,,,,mutect2;pindel;varscan2
PPP4R1,9989,BI,GRCh38,chr18,9595146,9595146,+,Silent,SNP,C,C,T,rs746130013,,TCGA-CD-5802-01A-11D-1600-08,TCGA-CD-5802-10A-01D-1600-08,,,,,,,,,Somatic,,,,,,,c1b44966-0f72-4c4f-8783-ab3ffe7f17b2,af722e36-4912-45c4-b431-a2ceff596bac,c.60G>A,p.Val20=,p.V20=,ENST00000400556,3/20,140,116,24,164,,,"PPP4R1,synonymous_variant,p.V20=,ENST00000400556,NM_001042388.3,c.60G>A,LOW,YES,,,-1;PPP4R1,5_prime_UTR_variant,,ENST00000581250,,c.-70G>A,MODIFIER,,,,-1;PPP4R1,intron_variant,,ENST00000400555,NM_001382562.1&NM_005134.4,c.53-44G>A,MODIFIER,,,,-1;PPP4R1,intron_variant,,ENST00000580745,,c.-26-44G>A,MODIFIER,,,,-1;PPP4R1,intron_variant,,ENST00000581835,,c.-26-44G>A,MODIFIER,,,,-1;PPP4R1,intron_variant,,ENST00000582240,,c.209-44G>A,MODIFIER,,,,-1;PPP4R1,intron_variant,,ENST00000584074,,c.-26-44G>A,MODIFIER,,,,-1;PPP4R1,non_coding_transcript_exon_variant,,ENST00000582933,,n.117G>A,MODIFIER,,,,-1;PPP4R1,non_coding_transcript_exon_variant,,ENST00000579415,,n.58G>A,MODIFIER,,,,-1;PPP4R1,intron_variant,,ENST00000578178,,n.84-44G>A,MODIFIER,,,,-1;PPP4R1,intron_variant,,ENST00000579638,,n.81-44G>A,MODIFIER,,,,-1;PPP4R1,intron_variant,,ENST00000583903,,n.64-44G>A,MODIFIER,,,,-1;PPP4R1,upstream_gene_variant,,ENST00000580583,,,MODIFIER,,,,-1;PPP4R1,synonymous_variant,p.V20=,ENST00000578875,,c.60G>A,LOW,,,,-1;PPP4R1,non_coding_transcript_exon_variant,,ENST00000580283,,n.57G>A,MODIFIER,,,,-1;PPP4R1,intron_variant,,ENST00000285124,,c.53-44G>A,MODIFIER,,,,-1;PPP4R1,intron_variant,,ENST00000577779,,n.82-44G>A,MODIFIER,,,,-1;PPP4R1,intron_variant,,ENST00000580182,,c.53-44G>A,MODIFIER,,,,-1;PPP4R1,intron_variant,,ENST00000583092,,c.*233-44G>A,MODIFIER,,,,-1;AP001381.1,downstream_gene_variant,,ENST00000584109,,,MODIFIER,YES,,,1",T,ENSG00000154845,ENST00000400556,Transcript,synonymous_variant,synonymous_variant,135/3923,60/2853,20/950,V,gtG/gtA,rs746130013;COSV53281699;COSV99553637,,-1,PPP4R1,HGNC,HGNC:9320,protein_coding,YES,CCDS42412.1,ENSP00000383402,Q8TF05.160,,UPI000006D6DE,Q8TF05-1,NM_001042388.3,NM_001042388.3,A2,,,,3/20,,PANTHER:PTHR10648;PANTHER:PTHR10648:SF8,,,,,,,,,8.027e-06,0.0,0.0,0.0,0.0,0.0,1.768e-05,0.0,0.0,1.768e-05,gnomAD_NFE,6.7646201387105975e-06,0.0,0.0,0.0,0.0,0.0,0.0,0.0,1.5431100109708495e-05,0.0,0.0,,,,0;1;1,,,,,,,,LOW,1.0,SNV,1.0,,0;1;1,,TCATCCACACC,7038f799-3e06-4998-b3c1-69f598faf0b4,836fb985-3ef2-4bd1-9e7c-092e897499f8,0aecac64-5982-4d76-8f31-958f6a00951d,,COSM4073670,N,Unknown,,,,muse;mutect2;varscan2
SUPT5H,6829,BI,GRCh38,chr19,39470176,39470176,+,Missense_Mutation,SNP,G,G,A,,,TCGA-CD-5802-01A-11D-1600-08,TCGA-CD-5802-10A-01D-1600-08,,,,,,,,,Somatic,,,,,,,c1b44966-0f72-4c4f-8783-ab3ffe7f17b2,af722e36-4912-45c4-b431-a2ceff596bac,c.1432G>A,p.Val478Met,p.V478M,ENST00000432763,17/30,280,217,62,385,,,"SUPT5H,missense_variant,p.V478M,ENST00000599117,,c.1432G>A,MODERATE,YES,deleterious(0),probably_damaging(0.998),1;SUPT5H,missense_variant,p.V474M,ENST00000359191,,c.1420G>A,MODERATE,,deleterious(0),probably_damaging(0.997),1;SUPT5H,missense_variant,p.V478M,ENST00000598725,NM_003169.3,c.1432G>A,MODERATE,,deleterious(0),probably_damaging(0.998),1;SUPT5H,missense_variant,p.V474M,ENST00000402194,NM_001130825.1&NM_001319991.2,c.1420G>A,MODERATE,,deleterious(0),probably_damaging(0.997),1;SUPT5H,missense_variant,p.V478M,ENST00000432763,NM_001111020.3&NM_001130824.2&NM_001319990.2,c.1432G>A,MODERATE,,deleterious(0),probably_damaging(0.998),1;SUPT5H,downstream_gene_variant,,ENST00000593727,,,MODIFIER,,,,1;SUPT5H,non_coding_transcript_exon_variant,,ENST00000599335,,n.1697G>A,MODIFIER,,,,1;SUPT5H,non_coding_transcript_exon_variant,,ENST00000598117,,n.614G>A,MODIFIER,,,,1;SUPT5H,upstream_gene_variant,,ENST00000596208,,,MODIFIER,,,,1;SUPT5H,downstream_gene_variant,,ENST00000598520,,,MODIFIER,,,,1",A,ENSG00000196235,ENST00000432763,Transcript,missense_variant,missense_variant,1575/3678,1432/3264,478/1087,V/M,Gtg/Atg,COSV63239286,,1,SUPT5H,HGNC,HGNC:11469,protein_coding,,CCDS12536.1,ENSP00000404029,O00267.192,,UPI000006D81A,O00267-1,NM_001111020.3;NM_001130824.2;NM_001319990.2,NM_001111020.3,P3,,deleterious(0),probably_damaging(0.998),17/30,,PDB-ENSP_mappings:2do3.A;PDB-ENSP_mappings:5oik.Z;PDB-ENSP_mappings:6gmh.Z;PDB-ENSP_mappings:6gml.Z;CDD:cd06083;PANTHER:PTHR11125;PANTHER:PTHR11125:SF7;Pfam:PF00467;PIRSF:PIRSF036945;Gene3D:2.30.30.30;SMART:SM00739;Superfamily:SSF50104,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1,,,,,,,,MODERATE,,SNV,1.0,,1,,ACCACGTGAAG,7038f799-3e06-4998-b3c1-69f598faf0b4,836fb985-3ef2-4bd1-9e7c-092e897499f8,0aecac64-5982-4d76-8f31-958f6a00951d,,COSM1393636,N,Unknown,,,,muse;mutect2;varscan2
LTBP4,8425,BI,GRCh38,chr19,40616996,40616996,+,Frame_Shift_Del,DEL,C,C,-,novel,,TCGA-CD-5802-01A-11D-1600-08,TCGA-CD-5802-10A-01D-1600-08,,,,,,,,,Somatic,,,,,,,c1b44966-0f72-4c4f-8783-ab3ffe7f17b2,af722e36-4912-45c4-b431-a2ceff596bac,c.3123del,p.Thr1042ArgfsTer51,p.T1042Rfs*51,ENST00000308370,23/33,66,55,11,62,,,"LTBP4,frameshift_variant,p.T1005Rfs*51,ENST00000204005,NM_003573.2,c.3012del,HIGH,,,,1;LTBP4,frameshift_variant,p.T975Rfs*51,ENST00000396819,NM_001042545.2,c.2922del,HIGH,,,,1;LTBP4,frameshift_variant,p.T1042Rfs*51,ENST00000308370,NM_001042544.1,c.3123del,HIGH,YES,,,1;LTBP4,frameshift_variant,p.T375Rfs*51,ENST00000243562,,c.1121del,HIGH,,,,1;LTBP4,frameshift_variant,p.T148Rfs*9,ENST00000597071,,c.439del,HIGH,,,,1;LTBP4,frameshift_variant,p.T123Rfs*9,ENST00000593463,,c.365del,HIGH,,,,1;LTBP4,frameshift_variant,p.T31Rfs*51,ENST00000622457,,c.89del,HIGH,,,,1;LTBP4,intron_variant,,ENST00000599724,,c.338-2349del,MODIFIER,,,,1;LTBP4,intron_variant,,ENST00000601032,,c.708-2349del,MODIFIER,,,,1;LTBP4,intron_variant,,ENST00000612121,,c.444-102del,MODIFIER,,,,1;LTBP4,intron_variant,,ENST00000618486,,c.256-102del,MODIFIER,,,,1;LTBP4,downstream_gene_variant,,ENST00000598055,,,MODIFIER,,,,1;LTBP4,non_coding_transcript_exon_variant,,ENST00000600499,,n.522del,MODIFIER,,,,1;LTBP4,non_coding_transcript_exon_variant,,ENST00000617753,,n.381del,MODIFIER,,,,1;LTBP4,non_coding_transcript_exon_variant,,ENST00000595665,,n.365del,MODIFIER,,,,1;LTBP4,non_coding_transcript_exon_variant,,ENST00000594448,,n.377del,MODIFIER,,,,1;LTBP4,non_coding_transcript_exon_variant,,ENST00000601464,,n.455del,MODIFIER,,,,1;LTBP4,intron_variant,,ENST00000318809,,n.337-2349del,MODIFIER,,,,1;LTBP4,intron_variant,,ENST00000595118,,n.576-2349del,MODIFIER,,,,1;LTBP4,intron_variant,,ENST00000596351,,n.304-2349del,MODIFIER,,,,1;LTBP4,intron_variant,,ENST00000597816,,n.306-2349del,MODIFIER,,,,1;LTBP4,intron_variant,,ENST00000610893,,n.411-102del,MODIFIER,,,,1;LTBP4,intron_variant,,ENST00000612845,,n.372-102del,MODIFIER,,,,1;LTBP4,intron_variant,,ENST00000622107,,n.272-102del,MODIFIER,,,,1;LTBP4,intron_variant,,ENST00000622565,,n.454-102del,MODIFIER,,,,1;LTBP4,downstream_gene_variant,,ENST00000546155,,,MODIFIER,,,,1;LTBP4,downstream_gene_variant,,ENST00000598717,,,MODIFIER,,,,1;LTBP4,downstream_gene_variant,,ENST00000602251,,,MODIFIER,,,,1",-,ENSG00000090006,ENST00000308370,Transcript,frameshift_variant,frameshift_variant,3121/4948,3121/4875,1041/1624,P/X,Ccc/cc,,,1,LTBP4,HGNC,HGNC:6717,protein_coding,YES,CCDS74369.1,ENSP00000311905,Q8N2S1.161,,UPI0000DACAC4,Q8N2S1-1,NM_001042544.1,,A2,,,,23/33,,Gene3D:2.10.25.10;Pfam:PF07645;PANTHER:PTHR24034;PANTHER:PTHR24034:SF43;SMART:SM00179;SMART:SM00181;Superfamily:SSF57184,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,HIGH,1.0,deletion,1.0,2.0,,1.0,TATCAGCCCACG,7038f799-3e06-4998-b3c1-69f598faf0b4,836fb985-3ef2-4bd1-9e7c-092e897499f8,0aecac64-5982-4d76-8f31-958f6a00951d,,,N,Unknown,,,,mutect2;pindel;varscan2
CKM,1158,BI,GRCh38,chr19,45311876,45311876,+,Silent,SNP,G,G,A,,,TCGA-CD-5802-01A-11D-1600-08,TCGA-CD-5802-10A-01D-1600-08,,,,,,,,,Somatic,,,,,,,c1b44966-0f72-4c4f-8783-ab3ffe7f17b2,af722e36-4912-45c4-b431-a2ceff596bac,c.526C>T,p.Leu176=,p.L176=,ENST00000221476,5/8,48,38,10,63,,,"CKM,synonymous_variant,p.L176=,ENST00000221476,NM_001824.5,c.526C>T,LOW,YES,,,-1",A,ENSG00000104879,ENST00000221476,Transcript,synonymous_variant,synonymous_variant,599/1556,526/1146,176/381,L,Ctg/Ttg,COSV55533029,,-1,CKM,HGNC,HGNC:1994,protein_coding,YES,CCDS12659.1,ENSP00000221476,P06732.199,,UPI000012DCC3,,NM_001824.5,NM_001824.5,P1,,,,5/8,,PDB-ENSP_mappings:1i0e.A;PDB-ENSP_mappings:1i0e.B;PDB-ENSP_mappings:1i0e.C;PDB-ENSP_mappings:1i0e.D;PROSITE_profiles:PS51510;CDD:cd00716;PANTHER:PTHR11547:SF27;PANTHER:PTHR11547;Gene3D:3.30.590.10;Pfam:PF00217;Superfamily:SSF55931,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1,,,,,,,,LOW,1.0,SNV,1.0,,1,,CTTCAGAGGGT,7038f799-3e06-4998-b3c1-69f598faf0b4,836fb985-3ef2-4bd1-9e7c-092e897499f8,0aecac64-5982-4d76-8f31-958f6a00951d,,COSM4079332,N,Unknown,,,,muse;mutect2;varscan2
ZNF419,79744,BI,GRCh38,chr19,57492259,57492259,+,Intron,SNP,C,C,T,,,TCGA-CD-5802-01A-11D-1600-08,TCGA-CD-5802-10A-01D-1600-08,,,,,,,,,Somatic,,,,,,,c1b44966-0f72-4c4f-8783-ab3ffe7f17b2,af722e36-4912-45c4-b431-a2ceff596bac,c.298+48C>T,,,ENST00000221735,,156,129,27,184,,,"ZNF419,3_prime_UTR_variant,,ENST00000518999,,c.*16C>T,MODIFIER,,,,1;ZNF419,3_prime_UTR_variant,,ENST00000520540,NM_001291745.2,c.*16C>T,MODIFIER,,,,1;ZNF419,intron_variant,,ENST00000221735,NM_024691.4,c.298+48C>T,MODIFIER,,,,1;ZNF419,intron_variant,,ENST00000347466,NM_001098494.2&NM_001291743.2,c.203-597C>T,MODIFIER,,,,1;ZNF419,intron_variant,,ENST00000354197,,c.262+48C>T,MODIFIER,,,,1;ZNF419,intron_variant,,ENST00000415379,NM_001098495.2&NM_001098496.2,c.161-597C>T,MODIFIER,,,,1;ZNF419,intron_variant,,ENST00000424930,NM_001098491.2,c.301+48C>T,MODIFIER,YES,,,1;ZNF419,intron_variant,,ENST00000426954,NM_001098492.2,c.262+48C>T,MODIFIER,,,,1;ZNF419,intron_variant,,ENST00000442920,NM_001098493.2,c.259+48C>T,MODIFIER,,,,1;ZNF419,intron_variant,,ENST00000519310,NM_001291744.2,c.35-597C>T,MODIFIER,,,,1;ZNF419,intron_variant,,ENST00000521137,,c.200-597C>T,MODIFIER,,,,1;ZNF419,intron_variant,,ENST00000521754,,c.164-597C>T,MODIFIER,,,,1;ZNF419,downstream_gene_variant,,ENST00000523138,,,MODIFIER,,,,1;ZNF419,downstream_gene_variant,,ENST00000523312,,,MODIFIER,,,,1;ZNF419,downstream_gene_variant,,ENST00000523882,,,MODIFIER,,,,1;ZNF419,intron_variant,,ENST00000522346,,n.3732+48C>T,MODIFIER,,,,1;ZNF419,intron_variant,,ENST00000523439,,n.1005+48C>T,MODIFIER,,,,1;AC003005.1,intron_variant,,ENST00000599674,,c.160+662C>T,MODIFIER,,,,1;AC003005.1,intron_variant,,ENST00000601674,,c.160+662C>T,MODIFIER,YES,,,1",T,ENSG00000105136,ENST00000221735,Transcript,intron_variant,intron_variant,,,,,,COSV99692556,,1,ZNF419,HGNC,HGNC:20648,protein_coding,,CCDS54326.1,ENSP00000221735,Q96HQ0.159,,UPI000040C68A,Q96HQ0-1,NM_024691.4,NM_024691.4,A2,,,,,4/4,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1,,,,,,,,MODIFIER,,SNV,1.0,,1,,GGATTCATATC,7038f799-3e06-4998-b3c1-69f598faf0b4,836fb985-3ef2-4bd1-9e7c-092e897499f8,0aecac64-5982-4d76-8f31-958f6a00951d,,,N,Unknown,,,,muse;mutect2;varscan2
EMILIN3,90187,BI,GRCh38,chr20,41362892,41362892,+,Missense_Mutation,SNP,A,A,G,,,TCGA-CD-5802-01A-11D-1600-08,TCGA-CD-5802-10A-01D-1600-08,,,,,,,,,Somatic,,,,,,,c1b44966-0f72-4c4f-8783-ab3ffe7f17b2,af722e36-4912-45c4-b431-a2ceff596bac,c.677T>C,p.Phe226Ser,p.F226S,ENST00000332312,4/4,71,53,18,104,,,"EMILIN3,missense_variant,p.F226S,ENST00000332312,NM_052846.2,c.677T>C,MODERATE,YES,deleterious(0),benign(0.413),-1;LPIN3,downstream_gene_variant,,ENST00000373257,NM_022896.3,,MODIFIER,,,,1;LPIN3,downstream_gene_variant,,ENST00000445975,,,MODIFIER,,,,1;LPIN3,downstream_gene_variant,,ENST00000632009,NM_001301860.2,,MODIFIER,YES,,,1;LPIN3,downstream_gene_variant,,ENST00000491528,,,MODIFIER,,,,1;LPIN3,downstream_gene_variant,,ENST00000496565,,,MODIFIER,,,,1",G,ENSG00000183798,ENST00000332312,Transcript,missense_variant,missense_variant,861/3791,677/2301,226/766,F/S,tTt/tCt,COSV60036138,,-1,EMILIN3,HGNC,HGNC:16123,protein_coding,YES,CCDS13316.1,ENSP00000332806,Q9NT22.133,,UPI00001D82E8,Q9NT22-1,NM_052846.2,NM_052846.2,P1,,deleterious(0),benign(0.413),4/4,,PANTHER:PTHR15427;PANTHER:PTHR15427:SF2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1,,,,,,,,MODERATE,1.0,SNV,1.0,,1,,CCCCAAAGCCC,7038f799-3e06-4998-b3c1-69f598faf0b4,836fb985-3ef2-4bd1-9e7c-092e897499f8,0aecac64-5982-4d76-8f31-958f6a00951d,,COSM4098428,N,Unknown,,,,muse;mutect2;varscan2
SREBF2,6721,BI,GRCh38,chr22,41866861,41866862,+,Frame_Shift_Del,DEL,GA,GA,-,novel,,TCGA-CD-5802-01A-11D-1600-08,TCGA-CD-5802-10A-01D-1600-08,,,,,,,,,Somatic,,,,,,,c1b44966-0f72-4c4f-8783-ab3ffe7f17b2,af722e36-4912-45c4-b431-a2ceff596bac,c.122_123del,p.Glu41ValfsTer3,p.E41Vfs*3,ENST00000361204,2/19,310,263,47,338,,,"SREBF2,frameshift_variant,p.E11Vfs*3,ENST00000612482,,c.32_33del,HIGH,,,,1;SREBF2,frameshift_variant,p.E41Vfs*3,ENST00000361204,NM_004599.4,c.122_123del,HIGH,YES,,,1;SREBF2,frameshift_variant,p.E41Vfs*3,ENST00000424354,,c.122_123del,HIGH,,,,1",-,ENSG00000198911,ENST00000361204,Transcript,frameshift_variant,frameshift_variant,285-286/5237,119-120/3426,40/1141,G/X,gGA/g,,,1,SREBF2,HGNC,HGNC:11290,protein_coding,YES,CCDS14023.1,ENSP00000354476,Q12772.204,A0A024R1Q0.52,UPI00001678D0,Q12772-1,NM_004599.4,NM_004599.4,P2,,,,2/19,,PANTHER:PTHR46062;PANTHER:PTHR46062:SF3,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,HIGH,1.0,deletion,1.0,3.0,,,AAGTGGGAGAGTT,7038f799-3e06-4998-b3c1-69f598faf0b4,836fb985-3ef2-4bd1-9e7c-092e897499f8,0aecac64-5982-4d76-8f31-958f6a00951d,,,N,Unknown,,,,pindel;varscan2
IDH3G,3421,BI,GRCh38,chrX,153786888,153786888,+,Silent,SNP,G,G,A,rs141309746,,TCGA-CD-5802-01A-11D-1600-08,TCGA-CD-5802-10A-01D-1600-08,,,,,,,,,Somatic,,,,,,,c1b44966-0f72-4c4f-8783-ab3ffe7f17b2,af722e36-4912-45c4-b431-a2ceff596bac,c.837C>T,p.Ile279=,p.I279=,ENST00000217901,10/13,93,51,41,103,,,"IDH3G,synonymous_variant,p.I279=,ENST00000370092,NM_174869.3,c.837C>T,LOW,,,,-1;IDH3G,synonymous_variant,p.I279=,ENST00000370093,,c.837C>T,LOW,,,,-1;IDH3G,synonymous_variant,p.I221=,ENST00000427365,,c.663C>T,LOW,,,,-1;IDH3G,synonymous_variant,p.I221=,ENST00000619865,,c.663C>T,LOW,,,,-1;IDH3G,synonymous_variant,p.I279=,ENST00000217901,NM_004135.4,c.837C>T,LOW,YES,,,-1;IDH3G,synonymous_variant,p.I256=,ENST00000444450,,c.768C>T,LOW,,,,-1;IDH3G,synonymous_variant,p.I85=,ENST00000454076,,c.255C>T,LOW,,,,-1;SRPK3,downstream_gene_variant,,ENST00000370100,,,MODIFIER,,,,1;SRPK3,downstream_gene_variant,,ENST00000370101,NM_014370.4,,MODIFIER,,,,1;SRPK3,downstream_gene_variant,,ENST00000370104,NM_001170760.2,,MODIFIER,,,,1;SRPK3,downstream_gene_variant,,ENST00000370108,,,MODIFIER,,,,1;SRPK3,downstream_gene_variant,,ENST00000393786,NM_001170761.1,,MODIFIER,,,,1;SRPK3,downstream_gene_variant,,ENST00000430541,,,MODIFIER,,,,1;IDH3G,downstream_gene_variant,,ENST00000444338,,,MODIFIER,,,,-1;SRPK3,downstream_gene_variant,,ENST00000458681,,,MODIFIER,,,,1;SRPK3,downstream_gene_variant,,ENST00000489426,,,MODIFIER,YES,,,1;IDH3G,downstream_gene_variant,,ENST00000461215,,,MODIFIER,,,,-1;IDH3G,downstream_gene_variant,,ENST00000491235,,,MODIFIER,,,,-1;IDH3G,downstream_gene_variant,,ENST00000495356,,,MODIFIER,,,,-1;IDH3G,downstream_gene_variant,,ENST00000497043,,,MODIFIER,,,,-1",A,ENSG00000067829,ENST00000217901,Transcript,synonymous_variant,synonymous_variant,886/1335,837/1182,279/393,I,atC/atT,rs141309746;COSV54207470,,-1,IDH3G,HGNC,HGNC:5386,protein_coding,YES,CCDS14730.1,ENSP00000217901,P51553.203,,UPI0000000DBC,P51553-1,NM_004135.4,NM_004135.4,P1,,,,10/13,,Gene3D:3.40.718.10;PDB-ENSP_mappings:5gre.B;PDB-ENSP_mappings:5grf.B;PDB-ENSP_mappings:5grh.B;PDB-ENSP_mappings:5gri.B;PDB-ENSP_mappings:5grl.B;PDB-ENSP_mappings:5yvt.B;PDB-ENSP_mappings:6l57.B;PDB-ENSP_mappings:6l59.B;Pfam:PF00180;PROSITE_patterns:PS00470;PANTHER:PTHR11835;PANTHER:PTHR11835:SF58;SMART:SM01329;Superfamily:SSF53659;TIGRFAM:TIGR00175,0.0003,0.0,0.0,0.0,0.0,0.0014,0.0002608,0.0,6.551e-05,0.0005326,0.0,0.0,0.0,6.247e-05,2.448e-05,0.0,0.0001048,0.0014,SAS,0.0002451649925205,0.0007111000013537,0.0,0.0,0.0,0.0,0.0,0.0,7.82212009653449e-05,0.0,0.0003653639869298,0.0007111000013537,afr,,0;1,,,,,,,,LOW,1.0,SNV,1.0,,0;1,,TTGACGATGTT,7038f799-3e06-4998-b3c1-69f598faf0b4,836fb985-3ef2-4bd1-9e7c-092e897499f8,0aecac64-5982-4d76-8f31-958f6a00951d,,COSM4107871,N,Unknown,,,,muse;mutect2;varscan2