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 COSMIC_Codon COSMIC_Gene Transcript_Id Exon ChromChange AAChange Genome_Plus_Minus_10_Bp Drug_Target TTotCov TVarCov NTotCov NVarCov dbSNPPopFreq COSMIC_Gene_Freq COSMIC_Site_Freq TVarRat NVarRat dbSNP_Strength dbSNP_AF dbSNP_PopFreq Confidence Algorithm GABRD 2563 hgsc.bcm.edu hg19 1 1960690 1960690 + Missense_Mutation SNP G G A novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . GABRD NM_000815 exon7 c.G832A p.A278T GTGCCCGCCAGGG . 56.0 9.0 74.0 0.0 . 49 . . . none . . PASS Atlas-SNP FGR 2268 hgsc.bcm.edu hg19 1 27943445 27943445 + Missense_Mutation SNP T T A novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . FGR NM_001042729 exon7 c.A605T p.K202I TCCAGTTTGCGGA . 139.0 29.0 199.0 0.0 . 39 . . . none . . PASS Atlas-SNP MRPS15 64960 hgsc.bcm.edu hg19 1 36921882 36921882 + Missense_Mutation SNP A A G novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . MRPS15 NM_031280 exon7 c.T542C p.I181T CAGCATATCTTCT . 72.0 22.0 67.0 0.0 . 21 . . . none . . PASS Atlas-SNP BCAR3 8412 hgsc.bcm.edu hg19 1 94033045 94033045 + Missense_Mutation SNP G G C novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . BCAR3 NM_001261409 exon11 c.C2090G p.S697C CATGTGGACTCTG . 63.0 14.0 99.0 0.0 . 62 . . . none . . PASS Atlas-SNP GON4L 54856 hgsc.bcm.edu hg19 1 155734744 155734744 + Missense_Mutation SNP A A G novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . GON4L NM_032292 exon21 c.T4520C p.M1507T TGATACATATTAC . 303.0 86.0 299.0 0.0 . 392 . . . none . . PASS Atlas-SNP GORAB 92344 hgsc.bcm.edu hg19 1 170508438 170508438 + Missense_Mutation SNP A A C novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . GORAB NM_152281 exon2 c.A224C p.K75T GCCAAAAACTTGG . 149.0 39.0 164.0 0.0 . 41 . . . none . . PASS Atlas-SNP EIF2D 1939 hgsc.bcm.edu hg19 1 206767112 206767112 + Missense_Mutation SNP C C T novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . EIF2D NM_006893 exon14 c.G1540A p.G514S CCAGACCATAGGC . 37.0 8.0 45.0 0.0 . 42 . . . none . . PASS Atlas-SNP TP53BP2 7159 hgsc.bcm.edu hg19 1 223983631 223983631 + Missense_Mutation SNP C C A novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . TP53BP2 NM_001031685 exon13 c.G2610T p.E870D GTACTCCTCCAGG . 72.0 19.0 81.0 0.0 . 144 . . . none . . PASS Atlas-SNP MYCN 4613 hgsc.bcm.edu hg19 2 16082258 16082258 + Silent SNP A A G novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . MYCN NM_005378 exon2 c.A72G p.L24L CTCGCTACAGCCC . 216.0 58.0 264.0 0.0 . 63 . . . none . . PASS Atlas-SNP DPY30 84661 hgsc.bcm.edu hg19 2 32264491 32264491 + Missense_Mutation SNP T T A novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . DPY30 NM_032574 exon2 c.A35T p.Q12L GATACCTGCGTTT . 103.0 29.0 117.0 0.0 . 6 . . . none . . PASS Atlas-SNP EPAS1 2034 hgsc.bcm.edu hg19 2 46607787 46607787 + Missense_Mutation SNP C C G novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . EPAS1 NM_001430 exon12 c.C1976G p.T659R AGCGCACAGAGTT . 76.0 17.0 90.0 0.0 . 83 . . . none . . PASS Atlas-SNP CNTNAP5 129684 hgsc.bcm.edu hg19 2 125175092 125175092 + Missense_Mutation SNP G G A novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 CNTNAP5,NS,haematopoietic_neoplasm,0,1 CNTNAP5 NM_130773 exon4 c.G454A p.V152I CGATTTGTTCGCT . 125.0 41.0 122.0 1.0 . 405 . . . none . . PASS Atlas-SNP CCDC141 285025 hgsc.bcm.edu hg19 2 179843225 179843225 + Nonsense_Mutation SNP C C A novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 .,2 CCDC141 NM_173648 exon3 c.G403T p.E135X CATTTTCAAAAAA . 100.0 16.0 127.0 0.0 . 362 . . . none . . PASS Atlas-SNP NEU2 4759 hgsc.bcm.edu hg19 2 233898967 233898967 + Silent SNP C C T novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . NEU2 NM_005383 exon2 c.C343T p.L115L CAGCAGCTGCAGA . 64.0 14.0 111.0 0.0 . 42 . . . none . . PASS Atlas-SNP HDAC11 79885 hgsc.bcm.edu hg19 3 13525052 13525052 + Silent SNP T T G novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . HDAC11 NM_024827 exon3 c.T240G p.L80L CTATCTTAATGAG . 105.0 65.0 180.0 0.0 . 39 . . . none . . PASS Atlas-SNP TRAK1 22906 hgsc.bcm.edu hg19 3 42218379 42218379 + Silent SNP G G A novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 TRAK1_ENST00000543338,NS,carcinoma,0,3 TRAK1 NM_001265608 exon3 c.G360A p.E120E TCTTGAGGAGGTA . 82.0 39.0 126.0 0.0 . 188 . . . none . . PASS Atlas-SNP SNRK 54861 hgsc.bcm.edu hg19 3 43388848 43388848 + Missense_Mutation SNP A A T novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . SNRK NM_017719 exon7 c.A1097T p.K366I CAACCAAAATTGA . 27.0 16.0 55.0 0.0 . 118 . . . none . . PASS Atlas-SNP SH3TC1 54436 hgsc.bcm.edu hg19 4 8230146 8230146 + Missense_Mutation SNP T T C novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . SH3TC1 NM_018986 exon12 c.T2725C p.F909L GCCAACTTCGGGG . 82.0 24.0 73.0 0.0 . 105 . . . none . . PASS Atlas-SNP NPFFR2 10886 hgsc.bcm.edu hg19 4 73012854 73012854 + Silent SNP C C G novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . NPFFR2 NM_004885 exon4 c.C894G p.S298S CAACTCCCAGAAT . 58.0 15.0 82.0 0.0 . 98 . . . none . . PASS Atlas-SNP FAM13A 10144 hgsc.bcm.edu hg19 4 89658657 89658657 + Missense_Mutation SNP T T A novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . FAM13A NM_014883 exon21 c.A2612T p.E871V TCGCCCTCGATAA . 85.0 24.0 115.0 0.0 . 181 . . . none . . PASS Atlas-SNP KIAA0922 23240 hgsc.bcm.edu hg19 4 154542029 154542029 + Nonsense_Mutation SNP C C A novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . KIAA0922 NM_001131007 exon27 c.C3689A p.S1230X CAGTCTCAAGGTG . 651.0 188.0 671.0 0.0 . 214 . . . none . . PASS Atlas-SNP F2R 2149 hgsc.bcm.edu hg19 5 76029290 76029290 + Missense_Mutation SNP A A G novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . F2R NM_001992 exon2 c.A1240G p.N414D TCTAGTAACCTGA . 121.0 21.0 143.0 0.0 . 58 . . . none . . PASS Atlas-SNP TMEM173 340061 hgsc.bcm.edu hg19 5 138855862 138855862 + Missense_Mutation SNP C C T rs117897081 bycluster;byfrequency;by1000genomes;alternate_allele TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . TMEM173 NM_198282 exon8 c.G1124A p.R375H TCCGTGCGGAGAG . 90.0 38.0 105.0 0.0 . 19 . . . alt C|0.995;A|0.005 . PASS Atlas-SNP UNC5A 90249 hgsc.bcm.edu hg19 5 176305475 176305475 + Splice_Site SNP G G A novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 UNC5A,NS,carcinoma,0,1 UNC5A NM_133369 exon13 c.2020-1G>A . CCATCAGGAGATC . 110.0 24.0 115.0 0.0 . 76 . . . none . . PASS Atlas-SNP COL19A1 1310 hgsc.bcm.edu hg19 6 70646796 70646796 + Silent SNP A A G novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . COL19A1 NM_001858 exon8 c.A867G p.P289P CATTCCAAACAAG . 102.0 28.0 122.0 0.0 . 232 . . . none . . PASS Atlas-SNP LIMK1 3984 hgsc.bcm.edu hg19 7 73535230 73535230 + Silent SNP G G A novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . LIMK1 NM_002314 exon15 c.G1632A p.G544G CATCGGGCGGGTG . 126.0 6.0 135.0 0.0 . 55 . . . none . . PASS Atlas-SNP SRRT 51593 hgsc.bcm.edu hg19 7 100485704 100485704 + Missense_Mutation SNP C C A novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . SRRT NM_015908 exon18 c.C2368A p.Q790K CCACACCAGACTC . 148.0 69.0 157.0 0.0 . 108 . . . none . . PASS Atlas-SNP ANK1 286 hgsc.bcm.edu hg19 8 41551436 41551436 + Missense_Mutation SNP C C T novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 ANK1,caecum,carcinoma,0,1 ANK1 NM_001142446 exon30 c.G3635A p.R1212H AGCAGGCGCAGGC . 161.0 37.0 176.0 0.0 . 497 . . . none . . PASS Atlas-SNP RFX3 5991 hgsc.bcm.edu hg19 9 3271084 3271084 + Missense_Mutation SNP C C G novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . RFX3 NM_134428 exon11 c.G1121C p.S374T ATCAGGCTAAATT . 122.0 35.0 111.0 0.0 . 156 . . . none . . PASS Atlas-SNP STXBP1 6812 hgsc.bcm.edu hg19 9 130438137 130438137 + Missense_Mutation SNP G G A novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . STXBP1 NM_001032221 exon14 c.G1165A p.A389T ATGCGAGCCATCG . 92.0 22.0 123.0 0.0 . 99 . . . none . . PASS Atlas-SNP ASB6 140459 hgsc.bcm.edu hg19 9 132400146 132400146 + Nonsense_Mutation SNP T T A novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . ASB6 NM_017873 exon6 c.A1189T p.K397X GGGCTTTGACCTT . 29.0 9.0 47.0 0.0 . 31 . . . none . . PASS Atlas-SNP ALOX5 240 hgsc.bcm.edu hg19 10 45936826 45936826 + Missense_Mutation SNP T T A novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . ALOX5 NM_000698 exon9 c.T1220A p.I407N TTGCAATCAACAC . 67.0 24.0 94.0 0.0 . 88 . . . none . . PASS Atlas-SNP NCOA4 8031 hgsc.bcm.edu hg19 10 51585173 51585173 + Silent SNP G G A novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . NCOA4 NM_001145261 exon9 c.G1320A p.K440K TGAGAAGGAGGCT . 151.0 47.0 175.0 0.0 . 58 . . . none . . PASS Atlas-SNP NUDT13 25961 hgsc.bcm.edu hg19 10 74879906 74879906 + Missense_Mutation SNP A A C novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . NUDT13 NM_015901 exon3 c.A214C p.S72R CGGCACAGCCTGT . 52.0 17.0 78.0 0.0 . 16 . . . none . . PASS Atlas-SNP ZMIZ1 57178 hgsc.bcm.edu hg19 10 80968102 80968102 + Missense_Mutation SNP A A T novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . ZMIZ1 NM_020338 exon6 c.A70T p.N24Y TTACAGAATCCTG . 63.0 16.0 70.0 0.0 . 101 . . . none . . PASS Atlas-SNP SORCS1 114815 hgsc.bcm.edu hg19 10 108371744 108371744 + Missense_Mutation SNP G G T novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . SORCS1 NM_001206572 exon22 c.C2958A p.N986K ATCCAGGTTTGGA . 158.0 44.0 161.0 0.0 . 534 . . . none . . PASS Atlas-SNP OR5P2 120065 hgsc.bcm.edu hg19 11 7818418 7818418 + Silent SNP T T A novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . OR5P2 NM_153444 exon1 c.A72T p.P24P AAGGATTGGATCA . 63.0 15.0 68.0 0.0 . 68 . . . none . . PASS Atlas-SNP OR5P2 120065 hgsc.bcm.edu hg19 11 7818419 7818419 + Missense_Mutation SNP G G A novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . OR5P2 NM_153444 exon1 c.C71T p.P24L AGGATTGGATCAT . 62.0 15.0 67.0 0.0 . 68 . . . none . . PASS Atlas-SNP OR5P2 120065 hgsc.bcm.edu hg19 11 7818420 7818420 + Missense_Mutation SNP G G T novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . OR5P2 NM_153444 exon1 c.C70A p.P24T GGATTGGATCATC . 61.0 15.0 67.0 0.0 . 68 . . . none . . PASS Atlas-SNP LGR4 55366 hgsc.bcm.edu hg19 11 27402259 27402259 + Splice_Site SNP C C G novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . LGR4 NM_018490 exon10 c.831-1G>C . AAATGTCTGTGAA . 223.0 73.0 232.0 0.0 . 87 . . . none . . PASS Atlas-SNP PLCB3 5331 hgsc.bcm.edu hg19 11 64034708 64034708 + Nonsense_Mutation SNP C C T novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . PLCB3 NM_000932 exon30 c.C3466T p.Q1156X CAGCAGCAGGTCC . 101.0 30.0 138.0 0.0 . 103 . . . none . . PASS Atlas-SNP NAALADL1 10004 hgsc.bcm.edu hg19 11 64813975 64813975 + Silent SNP G G A novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . NAALADL1 NM_005468 exon14 c.C1623T p.Y541Y GGTGGGGTAGATC . 138.0 31.0 184.0 0.0 . 58 . . . none . . PASS Atlas-SNP CLPB 81570 hgsc.bcm.edu hg19 11 72145214 72145214 + Missense_Mutation SNP T T A novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . CLPB NM_001258392 exon1 c.A305T p.D102V CAGCTGTCCTGTC . 69.0 15.0 96.0 0.0 . 45 . . . none . . PASS Atlas-SNP KCNE3 10008 hgsc.bcm.edu hg19 11 74168349 74168349 + Missense_Mutation SNP T T A novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . KCNE3 NM_005472 exon3 c.A260T p.K87M CTACGCTTGTCCA . 87.0 19.0 119.0 0.0 . 7 . . . none . . PASS Atlas-SNP KCNE3 10008 hgsc.bcm.edu hg19 11 74168350 74168350 + Nonsense_Mutation SNP T T A novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . KCNE3 NM_005472 exon3 c.A259T p.K87X TACGCTTGTCCAC . 87.0 19.0 120.0 0.0 . 7 . . . none . . PASS Atlas-SNP FZD4 8322 hgsc.bcm.edu hg19 11 86663362 86663362 + Missense_Mutation SNP T T C novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . FZD4 NM_012193 exon2 c.A436G p.S146G ATTTGCTGCAGTT . 101.0 20.0 146.0 0.0 . 52 . . . none . . PASS Atlas-SNP LRIG3 121227 hgsc.bcm.edu hg19 12 59268266 59268266 + Missense_Mutation SNP T T G novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . LRIG3 NM_153377 exon17 c.A2785C p.M929L AATACATAGGGCC . 130.0 48.0 146.0 0.0 . 120 . . . none . . PASS Atlas-SNP GPN3 51184 hgsc.bcm.edu hg19 12 110902939 110902939 + Silent SNP T T C novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . GPN3 NM_001164372 exon2 c.A246G p.A82A GTGTTCTGCTGCT . 106.0 18.0 111.0 0.0 . 37 . . . none . . PASS Atlas-SNP FAM155A 728215 hgsc.bcm.edu hg19 13 108518698 108518698 + Missense_Mutation SNP G G T novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . FAM155A NM_001080396 exon1 c.C247A p.Q83K GCTGCTGCTGCTG . 28.0 5.0 16.0 0.0 . 82 . . . none . . PASS Atlas-SNP THBS1 7057 hgsc.bcm.edu hg19 15 39877738 39877738 + Missense_Mutation SNP A A G novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . THBS1 NM_003246 exon7 c.A1094G p.D365G TTCCTGATGGAGA . 34.0 7.0 35.0 0.0 . 106 . . . none . . PASS Atlas-SNP SPINT1 6692 hgsc.bcm.edu hg19 15 41136856 41136856 + Missense_Mutation SNP C C A novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . SPINT1 NM_181642 exon2 c.C104A p.A35D CCCAGGCCGGGCC . 77.0 23.0 15.0 0.0 . 28 . . . none . . PASS Atlas-SNP LRRC57 255252 hgsc.bcm.edu hg19 15 42837381 42837381 + Missense_Mutation SNP C C T novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . LRRC57 NM_153260 exon5 c.G572A p.S191N AGCATGCTGAGCT . 74.0 26.0 85.0 0.0 . 20 . . . none . . PASS Atlas-SNP SHC4 399694 hgsc.bcm.edu hg19 15 49148178 49148178 + Missense_Mutation SNP G G T novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . SHC4 NM_203349 exon8 c.C1214A p.P405H TGTATGGGGCAGT . 117.0 28.0 145.0 0.0 . 70 . . . none . . PASS Atlas-SNP FBXL22 283807 hgsc.bcm.edu hg19 15 63889797 63889797 + Missense_Mutation SNP C C T novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . FBXL22 NM_203373 exon1 c.C206T p.P69L TGGGCCCGGCACT . 25.0 6.0 58.0 0.0 . 4 . . . none . . PASS Atlas-SNP LARP6 55323 hgsc.bcm.edu hg19 15 71128826 71128826 + Silent SNP T T C novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . LARP6 NM_018357 exon2 c.A219G p.G73G CTCACCTCCACTT . 70.0 24.0 81.0 0.0 . 43 . . . none . . PASS Atlas-SNP NTRK3 4916 hgsc.bcm.edu hg19 15 88680721 88680721 + Missense_Mutation SNP T T C novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . NTRK3 NM_001243101 exon7 c.A536G p.E179G TTGGCCTCCCCCT . 41.0 4.0 56.0 0.0 . 587 . . . none . . PASS Atlas-SNP PARN 5073 hgsc.bcm.edu hg19 16 14678281 14678281 + Splice_Site SNP T T C novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . PARN NM_001242992 exon16 c.868-2A>G . ATATCCTGCAAAC . 60.0 22.0 95.0 0.0 . 72 . . . none . . PASS Atlas-SNP ACSM2A 123876 hgsc.bcm.edu hg19 16 20489950 20489950 + Missense_Mutation SNP G G A novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . ACSM2A NM_001010845 exon11 c.G1232A p.G411D ACATTGGCATCAG . 67.0 24.0 89.0 0.0 . 120 . . . none . . PASS Atlas-SNP TNRC6A 27327 hgsc.bcm.edu hg19 16 24801321 24801321 + Missense_Mutation SNP C C G novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 TNRC6A,NS,carcinoma,0,1 TNRC6A NM_014494 exon6 c.C1358G p.P453R CTGGACCAAATAA . 102.0 25.0 106.0 0.0 . 171 . . . none . . PASS Atlas-SNP PYDC1 260434 hgsc.bcm.edu hg19 16 31228204 31228204 + Missense_Mutation SNP A A G novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . PYDC1 NM_152901 exon1 c.T146C p.I49T TCCACGATATCTA . 98.0 23.0 172.0 0.0 . 7 . . . none . . PASS Atlas-SNP N4BP1 9683 hgsc.bcm.edu hg19 16 48576974 48576974 + Silent SNP G G A novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . N4BP1 NM_153029 exon7 c.C2532T p.P844P TGGCATGGGCAGG . 68.0 9.0 76.0 0.0 . 121 . . . none . . PASS Atlas-SNP HS3ST3A1 9955 hgsc.bcm.edu hg19 17 13504436 13504436 + Missense_Mutation SNP G G T novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . HS3ST3A1 NM_006042 exon1 c.C11A p.P4Q GGGCCCGGAGGGG . 67.0 15.0 66.0 0.0 . 39 . . . none . . PASS Atlas-SNP ZNF830 91603 hgsc.bcm.edu hg19 17 33288777 33288777 + Silent SNP C C A novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . ZNF830 NM_052857 exon1 c.C192A p.L64L CGAGCTCCTGTGG . 128.0 53.0 117.0 0.0 . 26 . . . none . . PASS Atlas-SNP GGNBP2 79893 hgsc.bcm.edu hg19 17 34934557 34934557 + Silent SNP C C T novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 GGNBP2,NS,carcinoma,0,1 GGNBP2 NM_024835 exon7 c.C786T p.C262C TGTTTGCTGTGAA . 108.0 24.0 131.0 0.0 . 72 . . . none . . PASS Atlas-SNP RPRML 388394 hgsc.bcm.edu hg19 17 45056083 45056083 + Missense_Mutation SNP G G T novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . RPRML NM_203400 exon1 c.C291A p.S97R GATCATGCTCTCG . 102.0 28.0 106.0 0.0 . 2 . . . none . . PASS Atlas-SNP CEP192 55125 hgsc.bcm.edu hg19 18 13055803 13055803 + Missense_Mutation SNP A A T novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . CEP192 NM_032142 exon19 c.A3214T p.T1072S TTGAGTACCACAA . 42.0 14.0 67.0 0.0 . 340 . . . none . . PASS Atlas-SNP PHLPP1 23239 hgsc.bcm.edu hg19 18 60384475 60384475 + Missense_Mutation SNP T T A novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . PHLPP1 NM_194449 exon1 c.T1559A p.L520H GCTGCCTCATCCG . 46.0 16.0 80.0 0.0 . 164 . . . none . . PASS Atlas-SNP FEM1A 55527 hgsc.bcm.edu hg19 19 4792820 4792820 + Silent SNP C C A novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . FEM1A NM_018708 exon1 c.C954A p.A318A TGGGGCCCTTAAA . 108.0 32.0 159.0 0.0 . 41 . . . none . . PASS Atlas-SNP ZNF558 148156 hgsc.bcm.edu hg19 19 8922694 8922694 + Missense_Mutation SNP A A G novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . ZNF558 NM_144693 exon6 c.T472C p.F158L CTTTAAAACACTG . 72.0 9.0 84.0 0.0 . 43 . . . none . . PASS Atlas-SNP ZNF426 79088 hgsc.bcm.edu hg19 19 9639297 9639297 + Missense_Mutation SNP G G A novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . ZNF426 NM_024106 exon8 c.C1424T p.P475L TCATAGGGTTTTT . 114.0 29.0 147.0 0.0 . 56 . . . none . . PASS Atlas-SNP ICAM3 3385 hgsc.bcm.edu hg19 19 10444569 10444569 + Silent SNP T T A rs369252388 TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . ICAM3 NM_002162 exon7 c.A1608T p.T536T TGCTTCTGTCGGC . 121.0 24.0 162.0 0.0 . 29 . . . weak . . PASS Atlas-SNP CYP4F3 4051 hgsc.bcm.edu hg19 19 15752256 15752256 + Missense_Mutation SNP C C G novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . CYP4F3 NM_001199209 exon2 c.C31G p.L11V CTGGGCCTTTGGC . 64.0 16.0 84.0 0.0 . 69 . . . none . . PASS Atlas-SNP ZNF506 440515 hgsc.bcm.edu hg19 19 19905760 19905760 + Silent SNP G G C novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . ZNF506 NM_001099269 exon4 c.C936G p.P312P TTTGTAGGGTTTC . 39.0 10.0 36.0 0.0 . 36 . . . none . . PASS Atlas-SNP CYP2F1 1572 hgsc.bcm.edu hg19 19 41627458 41627458 + Missense_Mutation SNP C C T novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . CYP2F1 NM_000774 exon5 c.C580T p.R194C GATGAGCGTCTGC . 43.0 13.0 69.0 0.0 . 60 . . . none . . PASS Atlas-SNP PSG9 5678 hgsc.bcm.edu hg19 19 43772079 43772079 + Missense_Mutation SNP C C T novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . PSG9 NM_002784 exon2 c.G287A p.S96N CTTCCACTGTATG . 149.0 44.0 171.0 0.0 . 77 . . . none . . PASS Atlas-SNP ZNF836 162962 hgsc.bcm.edu hg19 19 52660313 52660313 + Missense_Mutation SNP A A T rs186568049 bycluster;by1000genomes;alternate_allele TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . ZNF836 NM_001102657 exon5 c.T623A p.L208H TTCTCAAGTTGGG . 177.0 48.0 180.0 0.0 . 158 . . . alt A|1.000;C|0.000 . PASS Atlas-SNP ZIM2 23619 hgsc.bcm.edu hg19 19 57286732 57286732 + Missense_Mutation SNP C C T novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . ZIM2 NM_015363 exon11 c.G908A p.G303E TCCTTTCCTAGAG . 88.0 21.0 112.0 0.0 . 511 . . . none . . PASS Atlas-SNP TIAM1 7074 hgsc.bcm.edu hg19 21 32639267 32639267 + Missense_Mutation SNP G G A novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . TIAM1 NM_003253 exon5 c.C22T p.H8Y CTACATGTTGACT . 24.0 7.0 50.0 0.0 . 522 . . . none . . PASS Atlas-SNP ASMTL 8623 hgsc.bcm.edu hg19 X 1540611 1540611 + Missense_Mutation SNP G G C rs374756969 alternate_allele TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . ASMTL NM_004192 exon9 c.C1185G p.I395M CTCTCGGATGGCA . 288.0 119.0 561.0 1.0 . 56 . . . alt . . PASS Atlas-SNP ACOT9 23597 hgsc.bcm.edu hg19 X 23723161 23723161 + Silent SNP G G A novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . ACOT9 NM_001037171 exon14 c.C1056T p.I352I AAACATGATGTCA . 161.0 100.0 166.0 0.0 . 33 . . . none . . PASS Atlas-SNP AR 367 hgsc.bcm.edu hg19 X 66765167 66765167 + Missense_Mutation SNP A A T novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . AR NM_000044 exon1 c.A179T p.Q60L AGCAGCAGCAGCA . 77.0 7.0 72.0 0.0 . 249 . . . none . . PASS Atlas-SNP ZMAT1 84460 hgsc.bcm.edu hg19 X 101152941 101152941 + Silent SNP A A T novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . ZMAT1 NM_001011657 exon5 c.T405A p.I135I CTGAGCAATAAGT . 76.0 36.0 86.0 0.0 . 143 . . . none . . PASS Atlas-SNP PNCK 139728 hgsc.bcm.edu hg19 X 152937048 152937048 + Missense_Mutation SNP G G C novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . PNCK NM_001039582 exon6 c.C743G p.A248G TTCCCAGCCTGGA . 66.0 39.0 101.0 0.0 . 70 . . . none . . PASS Atlas-SNP ND4 0 hgsc.bcm.edu hg19 MT 11411 11411 + Missense_Mutation SNP A A G novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . . ENST00000361381 exon1 c.A652G p.K218E CTCCCTAAAGCCC . 11.0 8.0 11.0 0.0 . . . . . none . . PASS Atlas-SNP ND5 0 hgsc.bcm.edu hg19 MT 13844 13844 + Missense_Mutation SNP A A G rs28562381 bycluster;alternate_allele TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . . ENST00000361567 exon1 c.A1508G p.D503G CCCTAGACCTCAA . 13.0 9.0 11.0 0.0 . . . . . alt . . PASS Atlas-SNP MCF2L 23263 hgsc.bcm.edu hg19 13 113719317 113719318 + Frame_Shift_Ins INS - - G novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . MCF2L NM_001112732 exon7 c.674_675insG p.L225fs . . 76.0 16.0 106.0 0.0 . 182 . 0.210526 0 none . . PASS Atlas-Indel,Pindel C12orf40 283461 hgsc.bcm.edu hg19 12 40076521 40076521 + Frame_Shift_Del DEL A A - novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . C12orf40 NM_001031748 exon8 c.794delC p.S265X . . 154.0 36.0 120.0 0.0 . 118 . 0.233766 0 none . . PASS Atlas-Indel,Pindel REV1 51455 hgsc.bcm.edu hg19 2 100019396 100019397 + Frame_Shift_Ins INS - - A novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . REV1 NM_016316 exon20 c.3340_3341insT p.D1114_G1115delinsX . . 98.0 27.0 124.0 0.0 . 100 . 0.27551 0 none . . PASS Atlas-Indel,Pindel PRDX6 9588 hgsc.bcm.edu hg19 1 173454533 173454534 + Frame_Shift_Ins INS - - AAAAAAA novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 PRDX6,bladder,carcinoma,0,2 PRDX6 NM_004905 exon3 c.286_287insAAAAAAA p.E96fs . . 134.0 10.0 152.0 0.0 . 20 . 0.0746269 0 none . . PASS Atlas-Indel,Pindel SETD2 29072 hgsc.bcm.edu hg19 3 47165390 47165391 + Frame_Shift_Ins INS - - A novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . SETD2 NM_014159 exon3 c.736_737insT p.V246fs . . 52.0 30.0 72.0 0.0 . 721 . 0.576923 0 none . . PASS Atlas-Indel,Pindel SLC24A2 25769 hgsc.bcm.edu hg19 9 19516367 19516367 + Frame_Shift_Del DEL A A - novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . SLC24A2 NM_020344 exon10 c.1771delC p.H591fs . . 86.0 29.0 97.0 0.0 . 93 . 0.337209 0 none . . PASS Atlas-Indel,Pindel SLC20A2 6575 hgsc.bcm.edu hg19 8 42302170 42302170 + Frame_Shift_Del DEL T T - novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . SLC20A2 NM_001257180 exon6 c.725delT p.I242fs . . 126.0 42.0 124.0 0.0 . 64 . 0.333333 0 none . . PASS Atlas-Indel,Pindel MTMR14 64419 hgsc.bcm.edu hg19 3 9724897 9724898 + Frame_Shift_Ins INS - - A novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . MTMR14 NM_001077525 exon10 c.933_934insA p.L311fs . . 143.0 67.0 291.0 0.0 . 43 . 0.468531 0 none . . PASS Atlas-INDEL PARP1 142 hgsc.bcm.edu hg19 1 226555997 226555999 + In_Frame_Del DEL GAG GAG - novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 GAG GAG . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . PARP1 NM_001618 exon16 c.2179_2181del p.727_727del . . 66.0 17.0 76.0 0.0 . 100 . 0.257576 0 none . . PASS Atlas-Indel,Pindel MTMR14 64419 hgsc.bcm.edu hg19 3 9724894 9724896 + In_Frame_Del DEL CCT CCT - novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 CCT CCT . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . MTMR14 NM_001077525 exon10 c.929_931del p.310_311del . . 141.0 71.0 289.0 0.0 . 43 . 0.503546 0 none . . PASS Atlas-INDEL ALS2 57679 hgsc.bcm.edu hg19 2 202572613 202572623 + Frame_Shift_Del DEL CGGGAATCTGA CGGGAATCTGA - novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 CGGGAATCTGA CGGGAATCTGA . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . ALS2 NM_020919 exon28 c.4373_4383del p.1458_1461del . . 251.0 22.0 329.0 0.0 . 172 . 0.0876494 0 none . . PASS Atlas-INDEL ALS2 57679 hgsc.bcm.edu hg19 2 202572610 202572610 + Frame_Shift_Del DEL G G - novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . ALS2 NM_020919 exon28 c.4386delT p.S1462fs . . 256.0 24.0 328.0 0.0 . 172 . 0.09375 0 none . . PASS Atlas-INDEL DLD 1738 hgsc.bcm.edu hg19 7 107556127 107556127 + Frame_Shift_Del DEL A A - novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . DLD NM_000108 exon9 c.860delG p.G287fs . . 125.0 14.0 127.0 0.0 . 72 . 0.112 0 none . . PASS Atlas-INDEL CDHR3 222256 hgsc.bcm.edu hg19 7 105673047 105673047 + Frame_Shift_Del DEL G G - novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . CDHR3 NM_152750 exon19 c.2561delT p.L854fs . . 170.0 37.0 175.0 0.0 . 153 . 0.217647 0 none . . PASS Atlas-Indel,Pindel PLCZ1 89869 hgsc.bcm.edu hg19 12 18876363 18876364 + Frame_Shift_Ins INS - - T novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . PLCZ1 NM_033123 exon4 c.249_250insA p.N83fs . . 171.0 46.0 108.0 0.0 . 107 . 0.269 . none . . PASS Pindel MTMR14 64419 hgsc.bcm.edu hg19 3 9724894 9724897 + Frame_Shift_Del DEL CCTG CCTG - novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 CCTG CCTG . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . MTMR14 NM_001077525 exon10 c.929_932del p.310_311del . . 144.0 54.0 291.0 0.0 . 43 . 0.375 . none . . PASS Pindel AFF4 27125 hgsc.bcm.edu hg19 5 132224787 132224791 + Frame_Shift_Del DEL GCTTT GCTTT - novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 GCTTT GCTTT . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . AFF4 NM_014423 exon14 c.2713_2717del p.905_906del . . 459.0 23.0 429.0 0.0 . 120 . 0.050 . none . . PASS Pindel ALS2 57679 hgsc.bcm.edu hg19 2 202572610 202572623 + Frame_Shift_Del DEL GATCGGGAATCTGA GATCGGGAATCTGA - novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 GATCGGGAATCTGA GATCGGGAATCTGA . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . ALS2 NM_020919 exon28 c.4373_4386del p.1458_1462del . . 274.0 32.0 339.0 0.0 . 172 . 0.117 . none . . PASS Pindel DLD 1738 hgsc.bcm.edu hg19 7 107556131 107556131 + Frame_Shift_Del DEL A A - novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . DLD NM_000108 exon9 c.864delA p.K288fs . . 122.0 12.0 116.0 0.0 . 72 . 0.098 . none . . PASS Pindel HOXB4 3214 hgsc.bcm.edu hg19 17 46655633 46655634 + In_Frame_Ins INS - - CTT novel TCGA-B1-A656-01A-11D-A31X-10 TCGA-B1-A656-10A-01D-A31X-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2ac9225b-09f2-40d9-8d53-3287fa4779b7 1b3cf7d6-8f3d-472a-958f-0e800ef04ce3 . HOXB4 NM_024015 exon1 c.49_50insAAG p.F17delinsKF . . 188.0 36.0 166.0 0.0 . 16 . 0.191 . none . . PASS Pindel