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 TEKT2 27285 hgsc.bcm.edu hg19 1 36552574 36552574 + Silent SNP C C T novel TCGA-PJ-A5Z9-01A-11D-A28G-10 TCGA-PJ-A5Z9-10A-01D-A28G-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0040144d-5bfe-4476-b511-2fa1fed81583 32635493-96c3-4fed-a9f7-85537363c7f0 . TEKT2 NM_014466 exon6 c.C675T p.N225N GTTCAACAAGGAC . 47.0 17.0 65.0 0.0 . 32 . . . none . . PASS Atlas-SNP SLC35D1 23169 hgsc.bcm.edu hg19 1 67519574 67519574 + Silent SNP C C A novel TCGA-PJ-A5Z9-01A-11D-A28G-10 TCGA-PJ-A5Z9-10A-01D-A28G-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0040144d-5bfe-4476-b511-2fa1fed81583 32635493-96c3-4fed-a9f7-85537363c7f0 . SLC35D1 NM_015139 exon1 c.G123T p.L41L CAGCTTCAGAAAC . 115.0 35.0 194.0 0.0 . 22 . . . none . . PASS Atlas-SNP C1orf173 127254 hgsc.bcm.edu hg19 1 75037280 75037280 + Missense_Mutation SNP C C A novel TCGA-PJ-A5Z9-01A-11D-A28G-10 TCGA-PJ-A5Z9-10A-01D-A28G-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0040144d-5bfe-4476-b511-2fa1fed81583 32635493-96c3-4fed-a9f7-85537363c7f0 . C1orf173 NM_001002912 exon14 c.G4114T p.A1372S TATTTGCTATTGT . 97.0 37.0 149.0 0.0 . 380 . . . none . . PASS Atlas-SNP ABCA4 24 hgsc.bcm.edu hg19 1 94546179 94546179 + Silent SNP G G A novel TCGA-PJ-A5Z9-01A-11D-A28G-10 TCGA-PJ-A5Z9-10A-01D-A28G-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0040144d-5bfe-4476-b511-2fa1fed81583 32635493-96c3-4fed-a9f7-85537363c7f0 . ABCA4 NM_000350 exon8 c.C954T p.I318I AGACAGGATGCCC . 97.0 30.0 138.0 0.0 . 275 . . . none . . PASS Atlas-SNP SLC30A7 148867 hgsc.bcm.edu hg19 1 101387350 101387350 + Missense_Mutation SNP A A G novel TCGA-PJ-A5Z9-01A-11D-A28G-10 TCGA-PJ-A5Z9-10A-01D-A28G-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0040144d-5bfe-4476-b511-2fa1fed81583 32635493-96c3-4fed-a9f7-85537363c7f0 . SLC30A7 NM_133496 exon8 c.A795G p.I265M GATGATAGCAGAT . 31.0 11.0 59.0 0.0 . 33 . . . none . . PASS Atlas-SNP HMCN1 83872 hgsc.bcm.edu hg19 1 186043967 186043967 + Missense_Mutation SNP G G T novel TCGA-PJ-A5Z9-01A-11D-A28G-10 TCGA-PJ-A5Z9-10A-01D-A28G-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0040144d-5bfe-4476-b511-2fa1fed81583 32635493-96c3-4fed-a9f7-85537363c7f0 . HMCN1 NM_031935 exon53 c.G8234T p.C2745F ATACTTGTGTAGC . 97.0 4.0 104.0 0.0 . 797 . . . none . . PASS Atlas-SNP IRF2BP2 359948 hgsc.bcm.edu hg19 1 234743060 234743060 + Silent SNP G G A novel TCGA-PJ-A5Z9-01A-11D-A28G-10 TCGA-PJ-A5Z9-10A-01D-A28G-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0040144d-5bfe-4476-b511-2fa1fed81583 32635493-96c3-4fed-a9f7-85537363c7f0 . IRF2BP2 NM_182972 exon2 c.C1587T p.F529F GAAGCAGAACTTG . 99.0 38.0 99.0 0.0 . 37 . . . none . . PASS Atlas-SNP GRB14 2888 hgsc.bcm.edu hg19 2 165477654 165477654 + Missense_Mutation SNP C C G novel TCGA-PJ-A5Z9-01A-11D-A28G-10 TCGA-PJ-A5Z9-10A-01D-A28G-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0040144d-5bfe-4476-b511-2fa1fed81583 32635493-96c3-4fed-a9f7-85537363c7f0 . GRB14 NM_004490 exon1 c.G166C p.G56R GGGTCCCGTCCGG . 53.0 30.0 2.0 0.0 . 73 . . . none . . PASS Atlas-SNP ATG9A 79065 hgsc.bcm.edu hg19 2 220085516 220085516 + Missense_Mutation SNP C C T novel TCGA-PJ-A5Z9-01A-11D-A28G-10 TCGA-PJ-A5Z9-10A-01D-A28G-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0040144d-5bfe-4476-b511-2fa1fed81583 32635493-96c3-4fed-a9f7-85537363c7f0 . ATG9A NM_001077198 exon15 c.G2467A p.V823M CGGGCACGGGCTC . 73.0 4.0 42.0 0.0 . 50 . . . none . . PASS Atlas-SNP DES 1674 hgsc.bcm.edu hg19 2 220283244 220283244 + Silent SNP G G A rs1058253 alternate_allele TCGA-PJ-A5Z9-01A-11D-A28G-10 TCGA-PJ-A5Z9-10A-01D-A28G-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0040144d-5bfe-4476-b511-2fa1fed81583 32635493-96c3-4fed-a9f7-85537363c7f0 . DES NM_001927 exon1 c.G60A p.G20G CGGCGGGGCCCCG . 29.0 21.0 3.0 0.0 . 53 . . . alt G|1.000;|0.000 . PASS Atlas-SNP DES 1674 hgsc.bcm.edu hg19 2 220283245 220283245 + Missense_Mutation SNP G G T novel TCGA-PJ-A5Z9-01A-11D-A28G-10 TCGA-PJ-A5Z9-10A-01D-A28G-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0040144d-5bfe-4476-b511-2fa1fed81583 32635493-96c3-4fed-a9f7-85537363c7f0 . DES NM_001927 exon1 c.G61T p.A21S GGCGGGGCCCCGG . 31.0 24.0 3.0 0.0 . 53 . . . none . . PASS Atlas-SNP KIF1A 547 hgsc.bcm.edu hg19 2 241696843 241696843 + Missense_Mutation SNP C C A novel TCGA-PJ-A5Z9-01A-11D-A28G-10 TCGA-PJ-A5Z9-10A-01D-A28G-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0040144d-5bfe-4476-b511-2fa1fed81583 32635493-96c3-4fed-a9f7-85537363c7f0 . KIF1A NM_001244008 exon27 c.G2751T p.E917D CTCATCCTCCTCC . 189.0 11.0 97.0 0.0 . 152 . . . none . . PASS Atlas-SNP SETD2 29072 hgsc.bcm.edu hg19 3 47164505 47164505 + Silent SNP G G T novel TCGA-PJ-A5Z9-01A-11D-A28G-10 TCGA-PJ-A5Z9-10A-01D-A28G-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0040144d-5bfe-4476-b511-2fa1fed81583 32635493-96c3-4fed-a9f7-85537363c7f0 . SETD2 NM_014159 exon3 c.C1621A p.R541R ACCCTCGTCGGAA . 77.0 4.0 42.0 0.0 . 721 . . . none . . PASS Atlas-SNP GMPPB 29925 hgsc.bcm.edu hg19 3 49759370 49759370 + Missense_Mutation SNP C C T rs71324991 TCGA-PJ-A5Z9-01A-11D-A28G-10 TCGA-PJ-A5Z9-10A-01D-A28G-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0040144d-5bfe-4476-b511-2fa1fed81583 32635493-96c3-4fed-a9f7-85537363c7f0 . GMPPB NM_013334 exon8 c.G979A p.E327K CCCTCTCCCCACC . 113.0 67.0 81.0 0.0 . 14 . . . weak C|0.500;T|0.500 0.500 PASS Atlas-SNP UBA7 7318 hgsc.bcm.edu hg19 3 49847782 49847782 + Missense_Mutation SNP A A T novel TCGA-PJ-A5Z9-01A-11D-A28G-10 TCGA-PJ-A5Z9-10A-01D-A28G-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0040144d-5bfe-4476-b511-2fa1fed81583 32635493-96c3-4fed-a9f7-85537363c7f0 . UBA7 NM_003335 exon13 c.T1547A p.L516Q GGATCCAGTGGGT . 254.0 148.0 270.0 0.0 . 64 . . . none . . PASS Atlas-SNP IGF2BP2 10644 hgsc.bcm.edu hg19 3 185542743 185542743 + Missense_Mutation SNP C C G novel TCGA-PJ-A5Z9-01A-11D-A28G-10 TCGA-PJ-A5Z9-10A-01D-A28G-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0040144d-5bfe-4476-b511-2fa1fed81583 32635493-96c3-4fed-a9f7-85537363c7f0 . IGF2BP2 NM_001007225 exon1 c.G6C p.M2I CTTGTTCATCATC . 169.0 34.0 88.0 0.0 . 69 . . . none . . PASS Atlas-SNP NKX3-2 579 hgsc.bcm.edu hg19 4 13545664 13545664 + Silent SNP G G A novel TCGA-PJ-A5Z9-01A-11D-A28G-10 TCGA-PJ-A5Z9-10A-01D-A28G-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0040144d-5bfe-4476-b511-2fa1fed81583 32635493-96c3-4fed-a9f7-85537363c7f0 . NKX3-2 NM_001189 exon1 c.C375T p.L125L CTGGCCGAGGCTC . 29.0 18.0 3.0 0.0 . 15 . . . none . . PASS Atlas-SNP NIPAL1 152519 hgsc.bcm.edu hg19 4 48037862 48037862 + Silent SNP T T C novel TCGA-PJ-A5Z9-01A-11D-A28G-10 TCGA-PJ-A5Z9-10A-01D-A28G-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0040144d-5bfe-4476-b511-2fa1fed81583 32635493-96c3-4fed-a9f7-85537363c7f0 . NIPAL1 NM_207330 exon6 c.T906C p.N302N CTTTAATACCTCT . 145.0 58.0 201.0 0.0 . 29 . . . none . . PASS Atlas-SNP MAP3K1 4214 hgsc.bcm.edu hg19 5 56170960 56170960 + Silent SNP G G T novel TCGA-PJ-A5Z9-01A-11D-A28G-10 TCGA-PJ-A5Z9-10A-01D-A28G-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0040144d-5bfe-4476-b511-2fa1fed81583 32635493-96c3-4fed-a9f7-85537363c7f0 . MAP3K1 NM_005921 exon10 c.G1788T p.L596L CCTGCTGTTGGCA . 72.0 4.0 96.0 0.0 . 355 . . . none . . PASS Atlas-SNP MSH3 4437 hgsc.bcm.edu hg19 5 79970928 79970928 + Missense_Mutation SNP A A T novel TCGA-PJ-A5Z9-01A-11D-A28G-10 TCGA-PJ-A5Z9-10A-01D-A28G-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0040144d-5bfe-4476-b511-2fa1fed81583 32635493-96c3-4fed-a9f7-85537363c7f0 . MSH3 NM_002439 exon7 c.A1154T p.N385I AGGGCAACATTTT . 98.0 41.0 148.0 0.0 . 129 . . . none . . PASS Atlas-SNP KDM3B 51780 hgsc.bcm.edu hg19 5 137717257 137717257 + Missense_Mutation SNP A A C novel TCGA-PJ-A5Z9-01A-11D-A28G-10 TCGA-PJ-A5Z9-10A-01D-A28G-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0040144d-5bfe-4476-b511-2fa1fed81583 32635493-96c3-4fed-a9f7-85537363c7f0 . KDM3B NM_016604 exon6 c.A758C p.D253A TGATGGATAATTC . 72.0 25.0 87.0 0.0 . 177 . . . none . . PASS Atlas-SNP CASP8AP2 9994 hgsc.bcm.edu hg19 6 90573643 90573643 + Missense_Mutation SNP T T C novel TCGA-PJ-A5Z9-01A-11D-A28G-10 TCGA-PJ-A5Z9-10A-01D-A28G-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0040144d-5bfe-4476-b511-2fa1fed81583 32635493-96c3-4fed-a9f7-85537363c7f0 . CASP8AP2 NM_001137667 exon7 c.T2215C p.Y739H TCAGATTATTGTG . 68.0 5.0 113.0 0.0 . 108 . . . none . . PASS Atlas-SNP REPS1 85021 hgsc.bcm.edu hg19 6 139262487 139262487 + Missense_Mutation SNP A A T novel TCGA-PJ-A5Z9-01A-11D-A28G-10 TCGA-PJ-A5Z9-10A-01D-A28G-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0040144d-5bfe-4476-b511-2fa1fed81583 32635493-96c3-4fed-a9f7-85537363c7f0 . REPS1 NM_001128617 exon8 c.T1120A p.L374M CTTCCAAATCAAT . 64.0 12.0 76.0 0.0 . 58 . . . none . . PASS Atlas-SNP PDE1C 5137 hgsc.bcm.edu hg19 7 31862809 31862809 + Missense_Mutation SNP C C A novel TCGA-PJ-A5Z9-01A-11D-A28G-10 TCGA-PJ-A5Z9-10A-01D-A28G-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0040144d-5bfe-4476-b511-2fa1fed81583 32635493-96c3-4fed-a9f7-85537363c7f0 . PDE1C NM_001191058 exon15 c.G1640T p.G547V TCTGAACCAGAGG . 117.0 38.0 100.0 0.0 . 465 . . . none . . PASS Atlas-SNP CSMD1 64478 hgsc.bcm.edu hg19 8 2824167 2824167 + Missense_Mutation SNP A A G novel TCGA-PJ-A5Z9-01A-11D-A28G-10 TCGA-PJ-A5Z9-10A-01D-A28G-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0040144d-5bfe-4476-b511-2fa1fed81583 32635493-96c3-4fed-a9f7-85537363c7f0 . CSMD1 NM_033225 exon58 c.T9025C p.Y3009H TCTTGTAGCCTTC . 122.0 50.0 211.0 0.0 . 1469 . . . none . . PASS Atlas-SNP NEFL 4747 hgsc.bcm.edu hg19 8 24813800 24813800 + Missense_Mutation SNP G G A novel TCGA-PJ-A5Z9-01A-11D-A28G-10 TCGA-PJ-A5Z9-10A-01D-A28G-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0040144d-5bfe-4476-b511-2fa1fed81583 32635493-96c3-4fed-a9f7-85537363c7f0 . NEFL NM_006158 exon1 c.C230T p.A77V ATGGCGGCTACCT . 173.0 13.0 174.0 0.0 . 47 . . . none . . PASS Atlas-SNP MATN2 4147 hgsc.bcm.edu hg19 8 99039960 99039960 + Missense_Mutation SNP G G T novel TCGA-PJ-A5Z9-01A-11D-A28G-10 TCGA-PJ-A5Z9-10A-01D-A28G-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0040144d-5bfe-4476-b511-2fa1fed81583 32635493-96c3-4fed-a9f7-85537363c7f0 . MATN2 NM_002380 exon14 c.G2259T p.R753S GGCCAGGCCCCTT . 137.0 52.0 124.0 0.0 . 165 . . . none . . PASS Atlas-SNP FOCAD 54914 hgsc.bcm.edu hg19 9 20988333 20988333 + Missense_Mutation SNP G G A novel TCGA-PJ-A5Z9-01A-11D-A28G-10 TCGA-PJ-A5Z9-10A-01D-A28G-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0040144d-5bfe-4476-b511-2fa1fed81583 32635493-96c3-4fed-a9f7-85537363c7f0 . . NM_017794 exon43 c.G4909A p.V1637I TCAGGCGTTTTGA . 91.0 8.0 103.0 0.0 . . . . . none . . PASS Atlas-SNP TOPORS 10210 hgsc.bcm.edu hg19 9 32541932 32541932 + Missense_Mutation SNP C C T novel TCGA-PJ-A5Z9-01A-11D-A28G-10 TCGA-PJ-A5Z9-10A-01D-A28G-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0040144d-5bfe-4476-b511-2fa1fed81583 32635493-96c3-4fed-a9f7-85537363c7f0 . TOPORS NM_005802 exon3 c.G2591A p.S864N CTTAGGCTCCGGG . 38.0 11.0 72.0 0.0 . 127 . . . none . . PASS Atlas-SNP FCN2 2220 hgsc.bcm.edu hg19 9 137777085 137777085 + Missense_Mutation SNP G G T novel TCGA-PJ-A5Z9-01A-11D-A28G-10 TCGA-PJ-A5Z9-10A-01D-A28G-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0040144d-5bfe-4476-b511-2fa1fed81583 32635493-96c3-4fed-a9f7-85537363c7f0 . FCN2 NM_004108 exon5 c.G302T p.G101V TCCCAGGCCCGCG . 45.0 16.0 54.0 0.0 . 55 . . . none . . PASS Atlas-SNP KCNT1 57582 hgsc.bcm.edu hg19 9 138594140 138594140 + Silent SNP C C G novel TCGA-PJ-A5Z9-01A-11D-A28G-10 TCGA-PJ-A5Z9-10A-01D-A28G-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0040144d-5bfe-4476-b511-2fa1fed81583 32635493-96c3-4fed-a9f7-85537363c7f0 . KCNT1 NM_001272003 exon1 c.C36G p.G12G GGGGGGCGTCTGC . 23.0 14.0 1.0 0.0 . 139 . . . none . . PASS Atlas-SNP ANK3 288 hgsc.bcm.edu hg19 10 61829169 61829169 + Missense_Mutation SNP C C T novel TCGA-PJ-A5Z9-01A-11D-A28G-10 TCGA-PJ-A5Z9-10A-01D-A28G-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0040144d-5bfe-4476-b511-2fa1fed81583 32635493-96c3-4fed-a9f7-85537363c7f0 . ANK3 NM_020987 exon37 c.G11470A p.V3824M CTTTCACTGGGTT . 57.0 23.0 76.0 0.0 . 703 . . . none . . PASS Atlas-SNP MMRN2 79812 hgsc.bcm.edu hg19 10 88703695 88703695 + Silent SNP G G A novel TCGA-PJ-A5Z9-01A-11D-A28G-10 TCGA-PJ-A5Z9-10A-01D-A28G-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0040144d-5bfe-4476-b511-2fa1fed81583 32635493-96c3-4fed-a9f7-85537363c7f0 . MMRN2 NM_024756 exon6 c.C846T p.A282A AGCCCTGGCCACG . 89.0 41.0 109.0 0.0 . 49 . . . none . . PASS Atlas-SNP RRP12 23223 hgsc.bcm.edu hg19 10 99160073 99160073 + Missense_Mutation SNP C C T novel TCGA-PJ-A5Z9-01A-11D-A28G-10 TCGA-PJ-A5Z9-10A-01D-A28G-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0040144d-5bfe-4476-b511-2fa1fed81583 32635493-96c3-4fed-a9f7-85537363c7f0 . RRP12 NM_001145114 exon2 c.G358A p.A120T TGTGGGCAGCCGA . 75.0 22.0 112.0 0.0 . 97 . . . none . . PASS Atlas-SNP STK32C 282974 hgsc.bcm.edu hg19 10 134036392 134036392 + Silent SNP C C T novel TCGA-PJ-A5Z9-01A-11D-A28G-10 TCGA-PJ-A5Z9-10A-01D-A28G-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0040144d-5bfe-4476-b511-2fa1fed81583 32635493-96c3-4fed-a9f7-85537363c7f0 . STK32C NM_173575 exon9 c.G1092A p.K364K CACCCTCTTCTCG . 51.0 19.0 2.0 0.0 . 61 . . . none . . PASS Atlas-SNP SLC22A18 5002 hgsc.bcm.edu hg19 11 2937874 2937874 + Missense_Mutation SNP G G T novel TCGA-PJ-A5Z9-01A-11D-A28G-10 TCGA-PJ-A5Z9-10A-01D-A28G-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0040144d-5bfe-4476-b511-2fa1fed81583 32635493-96c3-4fed-a9f7-85537363c7f0 . SLC22A18 NM_002555 exon6 c.G559T p.A187S ATCCTGGCTGCCC . 124.0 50.0 57.0 0.0 . 20 . . . none . . PASS Atlas-SNP MARS 4141 hgsc.bcm.edu hg19 12 57894254 57894254 + Silent SNP G G C novel TCGA-PJ-A5Z9-01A-11D-A28G-10 TCGA-PJ-A5Z9-10A-01D-A28G-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0040144d-5bfe-4476-b511-2fa1fed81583 32635493-96c3-4fed-a9f7-85537363c7f0 . MARS NM_004990 exon10 c.G1242C p.R414R GGCTCGGGGTGAC . 187.0 44.0 213.0 0.0 . 84 . . . none . . PASS Atlas-SNP NBEA 26960 hgsc.bcm.edu hg19 13 35770159 35770159 + Missense_Mutation SNP G G T novel TCGA-PJ-A5Z9-01A-11D-A28G-10 TCGA-PJ-A5Z9-10A-01D-A28G-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0040144d-5bfe-4476-b511-2fa1fed81583 32635493-96c3-4fed-a9f7-85537363c7f0 . NBEA NM_015678 exon31 c.G5086T p.G1696C AGTACAGGCCCTG . 111.0 57.0 100.0 0.0 . 340 . . . none . . PASS Atlas-SNP FSIP1 161835 hgsc.bcm.edu hg19 15 40056080 40056080 + Silent SNP C C T novel TCGA-PJ-A5Z9-01A-11D-A28G-10 TCGA-PJ-A5Z9-10A-01D-A28G-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0040144d-5bfe-4476-b511-2fa1fed81583 32635493-96c3-4fed-a9f7-85537363c7f0 . FSIP1 NM_152597 exon5 c.G501A p.E167E CATCTCCTCTTTA . 121.0 49.0 155.0 0.0 . 53 . . . none . . PASS Atlas-SNP NDUFAF1 51103 hgsc.bcm.edu hg19 15 41689069 41689069 + Silent SNP G G A novel TCGA-PJ-A5Z9-01A-11D-A28G-10 TCGA-PJ-A5Z9-10A-01D-A28G-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0040144d-5bfe-4476-b511-2fa1fed81583 32635493-96c3-4fed-a9f7-85537363c7f0 . NDUFAF1 NM_016013 exon2 c.C189T p.H63H TTTCTGGTGATCT . 60.0 24.0 77.0 0.0 . 39 . . . none . . PASS Atlas-SNP TICRR 90381 hgsc.bcm.edu hg19 15 90167321 90167321 + Silent SNP G G A novel TCGA-PJ-A5Z9-01A-11D-A28G-10 TCGA-PJ-A5Z9-10A-01D-A28G-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0040144d-5bfe-4476-b511-2fa1fed81583 32635493-96c3-4fed-a9f7-85537363c7f0 . . NM_152259 exon20 c.G3780A p.T1260T GGGCACGCCTCAG . 39.0 17.0 49.0 0.0 . . . . . none . . PASS Atlas-SNP ANKS3 124401 hgsc.bcm.edu hg19 16 4748510 4748510 + Missense_Mutation SNP G G T novel TCGA-PJ-A5Z9-01A-11D-A28G-10 TCGA-PJ-A5Z9-10A-01D-A28G-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0040144d-5bfe-4476-b511-2fa1fed81583 32635493-96c3-4fed-a9f7-85537363c7f0 . ANKS3 NM_133450 exon14 c.C1642A p.R548S GGGCGCGGTCCTG . 25.0 17.0 1.0 0.0 . 44 . . . none . . PASS Atlas-SNP GRIN2A 2903 hgsc.bcm.edu hg19 16 10273887 10273887 + Missense_Mutation SNP G G C novel TCGA-PJ-A5Z9-01A-11D-A28G-10 TCGA-PJ-A5Z9-10A-01D-A28G-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0040144d-5bfe-4476-b511-2fa1fed81583 32635493-96c3-4fed-a9f7-85537363c7f0 . GRIN2A NM_000833 exon3 c.C382G p.H128D CCCCATGAATGCC . 158.0 42.0 145.0 0.0 . 366 . . . none . . PASS Atlas-SNP DBNDD1 79007 hgsc.bcm.edu hg19 16 90072805 90072805 + Missense_Mutation SNP G G T novel TCGA-PJ-A5Z9-01A-11D-A28G-10 TCGA-PJ-A5Z9-10A-01D-A28G-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0040144d-5bfe-4476-b511-2fa1fed81583 32635493-96c3-4fed-a9f7-85537363c7f0 . DBNDD1 NM_024043 exon4 c.C475A p.P159T GCTCGGGGTCGCC . 62.0 16.0 38.0 0.0 . 9 . . . none . . PASS Atlas-SNP DNAH2 146754 hgsc.bcm.edu hg19 17 7727530 7727530 + Missense_Mutation SNP A A T novel TCGA-PJ-A5Z9-01A-11D-A28G-10 TCGA-PJ-A5Z9-10A-01D-A28G-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0040144d-5bfe-4476-b511-2fa1fed81583 32635493-96c3-4fed-a9f7-85537363c7f0 . DNAH2 NM_020877 exon75 c.A11570T p.H3857L CAGAGCACATGGG . 100.0 56.0 27.0 0.0 . 498 . . . none . . PASS Atlas-SNP SPAG5 10615 hgsc.bcm.edu hg19 17 26912886 26912886 + Missense_Mutation SNP T T C novel TCGA-PJ-A5Z9-01A-11D-A28G-10 TCGA-PJ-A5Z9-10A-01D-A28G-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0040144d-5bfe-4476-b511-2fa1fed81583 32635493-96c3-4fed-a9f7-85537363c7f0 . SPAG5 NM_006461 exon7 c.A1736G p.D579G ACCGCATCCTTGC . 79.0 48.0 74.0 0.0 . 92 . . . none . . PASS Atlas-SNP KRT13 3860 hgsc.bcm.edu hg19 17 39658844 39658844 + Silent SNP T T C novel TCGA-PJ-A5Z9-01A-11D-A28G-10 TCGA-PJ-A5Z9-10A-01D-A28G-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0040144d-5bfe-4476-b511-2fa1fed81583 32635493-96c3-4fed-a9f7-85537363c7f0 . KRT13 NM_002274 exon6 c.A1026G p.K342K CCCCGCTTTCTGG . 63.0 19.0 67.0 0.0 . 72 . . . none . . PASS Atlas-SNP CBX4 8535 hgsc.bcm.edu hg19 17 77807927 77807927 + Missense_Mutation SNP A A G rs200965379 TCGA-PJ-A5Z9-01A-11D-A28G-10 TCGA-PJ-A5Z9-10A-01D-A28G-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0040144d-5bfe-4476-b511-2fa1fed81583 32635493-96c3-4fed-a9f7-85537363c7f0 CBX4,uveal_tract,malignant_melanoma,0,1 CBX4 NM_003655 exon5 c.T1514C p.V505A GCCGCCACCGCCA . 34.0 22.0 2.0 1.0 . 40 . . . weak . . PASS Atlas-SNP TMC2 117532 hgsc.bcm.edu hg19 20 2592879 2592879 + Missense_Mutation SNP C C G novel TCGA-PJ-A5Z9-01A-11D-A28G-10 TCGA-PJ-A5Z9-10A-01D-A28G-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0040144d-5bfe-4476-b511-2fa1fed81583 32635493-96c3-4fed-a9f7-85537363c7f0 . TMC2 NM_080751 exon13 c.C1636G p.L546V TGGACTCTGTTTA . 78.0 10.0 63.0 0.0 . 121 . . . none . . PASS Atlas-SNP PANK2 80025 hgsc.bcm.edu hg19 20 3869791 3869791 + Missense_Mutation SNP C C T novel TCGA-PJ-A5Z9-01A-11D-A28G-10 TCGA-PJ-A5Z9-10A-01D-A28G-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0040144d-5bfe-4476-b511-2fa1fed81583 32635493-96c3-4fed-a9f7-85537363c7f0 . PANK2 NM_153638 exon1 c.C44T p.A15V GGGCGGCGCCGCC . 113.0 34.0 85.0 0.0 . 37 . . . none . . PASS Atlas-SNP KRTAP19-5 337972 hgsc.bcm.edu hg19 21 31874285 31874285 + Missense_Mutation SNP C C T rs370535457 TCGA-PJ-A5Z9-01A-11D-A28G-10 TCGA-PJ-A5Z9-10A-01D-A28G-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0040144d-5bfe-4476-b511-2fa1fed81583 32635493-96c3-4fed-a9f7-85537363c7f0 . KRTAP19-5 NM_181611 exon1 c.G124A p.G42R AGCCTCCGTAGCC . 48.0 34.0 172.0 0.0 . 32 . . . weak . . PASS Atlas-SNP TBL1X 6907 hgsc.bcm.edu hg19 X 9683003 9683003 + Missense_Mutation SNP C C T novel TCGA-PJ-A5Z9-01A-11D-A28G-10 TCGA-PJ-A5Z9-10A-01D-A28G-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0040144d-5bfe-4476-b511-2fa1fed81583 32635493-96c3-4fed-a9f7-85537363c7f0 . TBL1X NM_001139466 exon17 c.C1667T p.A556V GGAACGCCCGAGG . 178.0 81.0 272.0 0.0 . 103 . . . none . . PASS Atlas-SNP PHKA1 5255 hgsc.bcm.edu hg19 X 71802352 71802352 + Missense_Mutation SNP G G A novel TCGA-PJ-A5Z9-01A-11D-A28G-10 TCGA-PJ-A5Z9-10A-01D-A28G-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0040144d-5bfe-4476-b511-2fa1fed81583 32635493-96c3-4fed-a9f7-85537363c7f0 . PHKA1 NM_002637 exon31 c.C3394T p.L1132F GGACAAGGATGGC . 293.0 86.0 417.0 1.0 . 129 . . . none . . PASS Atlas-SNP GPR50 9248 hgsc.bcm.edu hg19 X 150348665 150348665 + Missense_Mutation SNP G G A novel TCGA-PJ-A5Z9-01A-11D-A28G-10 TCGA-PJ-A5Z9-10A-01D-A28G-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0040144d-5bfe-4476-b511-2fa1fed81583 32635493-96c3-4fed-a9f7-85537363c7f0 . GPR50 NM_004224 exon2 c.G610A p.V204M CTCATCGTGGGTT . 43.0 12.0 80.0 0.0 . 195 . . . none . . PASS Atlas-SNP RENBP 5973 hgsc.bcm.edu hg19 X 153200791 153200791 + Missense_Mutation SNP G G T novel TCGA-PJ-A5Z9-01A-11D-A28G-10 TCGA-PJ-A5Z9-10A-01D-A28G-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0040144d-5bfe-4476-b511-2fa1fed81583 32635493-96c3-4fed-a9f7-85537363c7f0 . RENBP NM_002910 exon11 c.C1232A p.P411H GGGGCGGGGCGGC . 8.0 4.0 0.0 0.0 . 69 . . . none . . PASS Atlas-SNP SREBF2 6721 hgsc.bcm.edu hg19 22 42289217 42289217 + Frame_Shift_Del DEL T T - novel TCGA-PJ-A5Z9-01A-11D-A28G-10 TCGA-PJ-A5Z9-10A-01D-A28G-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0040144d-5bfe-4476-b511-2fa1fed81583 32635493-96c3-4fed-a9f7-85537363c7f0 . SREBF2 NM_004599 exon12 c.2304delG p.K768fs . . 70.0 24.0 97.0 0.0 . 99 . 0.342857 0 none . . PASS Atlas-Indel,Pindel PLEC 5339 hgsc.bcm.edu hg19 8 145024821 145024825 + Frame_Shift_Del DEL CACCT CACCT - novel TCGA-PJ-A5Z9-01A-11D-A28G-10 TCGA-PJ-A5Z9-10A-01D-A28G-10 CACCT CACCT . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0040144d-5bfe-4476-b511-2fa1fed81583 32635493-96c3-4fed-a9f7-85537363c7f0 . PLEC NM_201380 exon1 c.51_55del p.17_19del . . 46.0 17.0 3.0 0.0 . 1144 . 0.369565 0 none . . PASS Atlas-Indel,Pindel VAPB 9217 hgsc.bcm.edu hg19 20 57009683 57009684 + Frame_Shift_Ins INS - - C novel TCGA-PJ-A5Z9-01A-11D-A28G-10 TCGA-PJ-A5Z9-10A-01D-A28G-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0040144d-5bfe-4476-b511-2fa1fed81583 32635493-96c3-4fed-a9f7-85537363c7f0 . VAPB NM_004738 exon3 c.237_238insC p.D79fs . . 79.0 21.0 89.0 0.0 . 21 . 0.265823 0 none . . PASS Atlas-Indel,Pindel IGFLR1 79713 hgsc.bcm.edu hg19 19 36230984 36230986 + In_Frame_Del DEL CGG CGG - novel TCGA-PJ-A5Z9-01A-11D-A28G-10 TCGA-PJ-A5Z9-10A-01D-A28G-10 CGG CGG . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0040144d-5bfe-4476-b511-2fa1fed81583 32635493-96c3-4fed-a9f7-85537363c7f0 . IGFLR1 NM_024660 exon4 c.347_349del p.116_117del . . 34.0 11.0 44.0 0.0 . 28 . 0.323529 0 none . . PASS Atlas-INDEL SLC14A1 6563 hgsc.bcm.edu hg19 18 43316457 43316458 + Frame_Shift_Ins INS - - A novel TCGA-PJ-A5Z9-01A-11D-A28G-10 TCGA-PJ-A5Z9-10A-01D-A28G-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0040144d-5bfe-4476-b511-2fa1fed81583 32635493-96c3-4fed-a9f7-85537363c7f0 . SLC14A1 NM_001146037 exon5 c.675_676insA p.S225fs . . 128.0 51.0 156.0 0.0 . 84 . 0.398438 0 none . . PASS Atlas-Indel,Pindel MIA3 375056 hgsc.bcm.edu hg19 1 222803477 222803477 + Frame_Shift_Del DEL A A - novel TCGA-PJ-A5Z9-01A-11D-A28G-10 TCGA-PJ-A5Z9-10A-01D-A28G-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0040144d-5bfe-4476-b511-2fa1fed81583 32635493-96c3-4fed-a9f7-85537363c7f0 .,1 MIA3 NM_198551 exon4 c.2914delG p.E972fs . . 73.0 32.0 76.0 0.0 . 167 . 0.438356 0 none . . PASS Atlas-Indel,Pindel