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- #version gdc-1.0.0
- #annotation.spec gdc-2.0.0-aliquot-merged-masked
- #contigs chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX,chrY,chrM
- #sort.order BarcodesAndCoordinate
- #filedate 20220516
- #normal.aliquot af722e36-4912-45c4-b431-a2ceff596bac
- #tumor.aliquot c1b44966-0f72-4c4f-8783-ab3ffe7f17b2
- 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 SNV 1 1 1 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 SNV 1 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 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 2.0301500626374036e-05 0.0 0.0 0.00013253799988888204 0.0 0.0 0.0 0.0 1.5435900422744453e-05 0.0 0.0 0.00013253799988888204 amr 0;1 MODERATE SNV 1 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 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 SNV 1 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 2.4309600121341646e-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 SNV 1 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 SNV 1 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 insertion 1 9 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;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 0.00030303001403808594 0.0 0.0 0.0 0.0 0.0 0.0 0;1 HIGH 1 SNV 1 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 SNV 2 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 SNV 1 1 1 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 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 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 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;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 SNV 1 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 SNV 1 1 1 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 1 1 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 SNV 1 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 1 1 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 1 1 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 0.00010143499821424484 0.0002920420083682984 0.0 0.0 0.0 0.0 0.0 0.0 3.086610013269819e-05 0.0004950499860569835 0.0 0.0002920420083682984 afr LOW 1 SNV 1 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 SNV 1 1 1 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 -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 4.8642901674611494e-05 0.0 0.0 0.0 0.00020145000598859042 0.0 0.0 3.086229844484478e-05 0.0 0.0 4.8642901674611494e-05 afr 0;1 MODIFIER SNV 2 0;1 1 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 0.00010800499876495451 0.0 0.0006249999860301614 0.0006249999860301614 sas 0;1 MODERATE 1 SNV 5 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 SNV 5 1 1 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 SNV 1 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;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 SNV 1 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 SNV 1 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 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 6.7570299506769516e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.00020824700186494738 0;1;1 MODERATE 1 SNV 1 0;1;1 1 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 1 1 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 SNV 1 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 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 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 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 1 1 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;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 SNV 1 1 1 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 1 1 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 SNV 1 1 1 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 SNV 5 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 SNV 5 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 1.3519699677999597e-05 2.4310800654347986e-05 0.0 0.0 0.0 0.0 9.419739944860339e-05 0.0 0.0 0.0 0.0 0;1;1 MODERATE SNV 1 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 4.6296299842651933e-05 0.0 0.0 4.862869900534861e-05 afr LOW 1 SNV 1 1 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 deletion 1 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 SNV 1 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 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 deletion 1 2 1 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 SNV 1 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 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 SNV 1 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 deletion 1 3 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 0.00024516499252058566 0.0007111000013537705 0.0 0.0 0.0 0.0 0.0 0.0 7.82212009653449e-05 0.0 0.0003653639869298786 0.0007111000013537705 afr 0;1 LOW 1 SNV 1 0;1 TTGACGATGTT 7038f799-3e06-4998-b3c1-69f598faf0b4 836fb985-3ef2-4bd1-9e7c-092e897499f8 0aecac64-5982-4d76-8f31-958f6a00951d COSM4107871 N Unknown muse;mutect2;varscan2
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