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 CLCA2 9635 hgsc.bcm.edu hg19 1 86890015 86890015 + Silent SNP C C T novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . CLCA2 NM_006536 exon1 c.C85T p.L29L CCATTCCTGGGAG . 55.0 35.0 47.0 0.0 . 102 . . . none . . PASS Atlas-SNP ADAR 103 hgsc.bcm.edu hg19 1 154574741 154574741 + Missense_Mutation SNP A A G novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . ADAR NM_015840 exon2 c.T377C p.L126P GAGGAAAGGCAAT . 41.0 24.0 94.0 0.0 . 113 . . . none . . PASS Atlas-SNP MIA3 375056 hgsc.bcm.edu hg19 1 222838735 222838735 + Missense_Mutation SNP G G T novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . MIA3 NM_198551 exon28 c.G5498T p.R1833L ACCCTCGGGGATT . 185.0 9.0 315.0 0.0 . 167 . . . none . . PASS Atlas-SNP CCT7 10574 hgsc.bcm.edu hg19 2 73471795 73471795 + Silent SNP G G T novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . CCT7 NM_006429 exon6 c.G570T p.L190L TTTGCTGCAGCTT . 38.0 12.0 39.0 0.0 . 60 . . . none . . PASS Atlas-SNP GORASP2 26003 hgsc.bcm.edu hg19 2 171806790 171806790 + Missense_Mutation SNP T T C novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . GORASP2 NM_015530 exon4 c.T425C p.V142A ATACAGTCATGAA . 76.0 32.0 29.0 0.0 . 40 . . . none . . PASS Atlas-SNP TTN 7273 hgsc.bcm.edu hg19 2 179411556 179411556 + Silent SNP A A G novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . TTN NM_001267550 exon341 c.T94599C p.D31533D GCCTCCATCATAC . 44.0 22.0 17.0 0.0 . 18412 . . . none . . PASS Atlas-SNP SF3B1 23451 hgsc.bcm.edu hg19 2 198269882 198269882 + Missense_Mutation SNP G G C novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . SF3B1 NM_012433 exon11 c.C1457G p.T486R CTAAGTGTTGATT . 42.0 4.0 29.0 0.0 . 1038 . . . none . . PASS Atlas-SNP SATB2 23314 hgsc.bcm.edu hg19 2 200193570 200193570 + Missense_Mutation SNP C C A novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . SATB2 NM_015265 exon9 c.G1237T p.V413L GGTTTACTAGAAG . 46.0 11.0 16.0 0.0 . 134 . . . none . . PASS Atlas-SNP NOP58 51602 hgsc.bcm.edu hg19 2 203155146 203155146 + Silent SNP T T C novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . NOP58 NM_015934 exon7 c.T600C p.D200D TTCAGATAATTTA . 76.0 31.0 58.0 0.0 . 41 . . . none . . PASS Atlas-SNP CYP27A1 1593 hgsc.bcm.edu hg19 2 219677361 219677361 + Missense_Mutation SNP G G T novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 CYP27A1,NS,malignant_melanoma,-1,1 CYP27A1 NM_000784 exon4 c.G733T p.G245W TCCATCGGGTTAA . 328.0 15.0 528.0 1.0 . 52 . . . none . . PASS Atlas-SNP MLH1 4292 hgsc.bcm.edu hg19 3 37067255 37067255 + Missense_Mutation SNP G G T rs63750361 bycluster;byfrequency;alternate_allele TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . MLH1 NM_000249 exon12 c.G1166T p.R389L ATTCCCGGGAACA . 186.0 12.0 206.0 0.0 . 226 . . . alt G|1.000;A|0.000 . PASS Atlas-SNP PBRM1 55193 hgsc.bcm.edu hg19 3 52588791 52588791 + Missense_Mutation SNP G G T novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . PBRM1 NM_018313 exon27 c.C4237A p.P1413T GGTGGGGTGGAGG . 39.0 19.0 47.0 0.0 . 1252 . . . none . . PASS Atlas-SNP CLDN18 51208 hgsc.bcm.edu hg19 3 137742626 137742626 + Missense_Mutation SNP A A T novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . CLDN18 NM_016369 exon2 c.A347T p.N116I AAGCCAACATGAC . 68.0 22.0 89.0 0.0 . 33 . . . none . . PASS Atlas-SNP FNDC3B 64778 hgsc.bcm.edu hg19 3 171965496 171965496 + Silent SNP C C A rs139712731 bycluster;byfrequency;alternate_allele TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . FNDC3B NM_001135095 exon5 c.C438A p.T146T TGTTACCGGACCT . 145.0 8.0 168.0 0.0 . 118 . . . alt C|0.999;T|0.001 . PASS Atlas-SNP TMEM41A 90407 hgsc.bcm.edu hg19 3 185209397 185209397 + Missense_Mutation SNP T T A novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 .,1 TMEM41A NM_080652 exon5 c.A723T p.K241N ACTAAATTTTTTA . 95.0 41.0 75.0 0.0 . 18 . . . none . . PASS Atlas-SNP FGFR3 2261 hgsc.bcm.edu hg19 4 1806088 1806088 + Silent SNP G G T novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 FGFR3,bladder,carcinoma,0,6 FGFR3 NM_001163213 exon9 c.G1113T p.A371A CGAGGCGGGCAGT . 166.0 8.0 289.0 0.0 . 3320 . . . none . . PASS Atlas-SNP SLC10A6 345274 hgsc.bcm.edu hg19 4 87749228 87749228 + Missense_Mutation SNP G G C novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . SLC10A6 NM_197965 exon4 c.C679G p.L227V TGGTCAGAAGGGT . 45.0 16.0 55.0 0.0 . 40 . . . none . . PASS Atlas-SNP CAMK2D 817 hgsc.bcm.edu hg19 4 114434488 114434488 + Silent SNP G G A novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . CAMK2D NM_172128 exon12 c.C942T p.F314F ACCTGAGAAATTC . 113.0 42.0 84.0 0.0 . 55 . . . none . . PASS Atlas-SNP NPY1R 4886 hgsc.bcm.edu hg19 4 164246582 164246582 + Missense_Mutation SNP C C A novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . NPY1R NM_000909 exon3 c.G1028T p.R343L TCATCCCGAGACC . 188.0 8.0 113.0 0.0 . 72 . . . none . . PASS Atlas-SNP TLR3 7098 hgsc.bcm.edu hg19 4 187004092 187004092 + Missense_Mutation SNP A A C novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . TLR3 NM_003265 exon4 c.A1252C p.K418Q AAGAATAAAATCT . 79.0 26.0 62.0 0.0 . 83 . . . none . . PASS Atlas-SNP ZFR 51663 hgsc.bcm.edu hg19 5 32403408 32403408 + Missense_Mutation SNP G G A novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . ZFR NM_016107 exon8 c.C1319T p.S440L GGCTTTGAAGCAG . 160.0 70.0 102.0 0.0 . 98 . . . none . . PASS Atlas-SNP PIK3R1 5295 hgsc.bcm.edu hg19 5 67576767 67576767 + Silent SNP T T G novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . PIK3R1 NM_181523 exon7 c.T849G p.T283T TAATACTGAAAAC . 61.0 18.0 41.0 0.0 . 869 . . . none . . PASS Atlas-SNP PAPD4 167153 hgsc.bcm.edu hg19 5 78975410 78975410 + Missense_Mutation SNP G G C novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . PAPD4 NM_173797 exon14 c.G1217C p.S406T GGAATAGTCAAAT . 73.0 33.0 57.0 0.0 . 51 . . . none . . PASS Atlas-SNP NELFE 7936 hgsc.bcm.edu hg19 6 31922209 31922209 + Silent SNP T T C novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . . NM_002904 exon8 c.A753G p.S251S AGGGAATGAATCC . 88.0 30.0 109.0 0.0 . . . . . none . . PASS Atlas-SNP EYS 346007 hgsc.bcm.edu hg19 6 66204808 66204808 + Missense_Mutation SNP T T G novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . EYS NM_001142801 exon4 c.A496C p.N166H TCACATTTAGTCG . 97.0 32.0 54.0 0.0 . 527 . . . none . . PASS Atlas-SNP ETV1 2115 hgsc.bcm.edu hg19 7 13971323 13971323 + Silent SNP C C G novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . ETV1 NM_004956 exon9 c.G606C p.T202T TGGCATCGTCGGC . 45.0 17.0 46.0 0.0 . 138 . . . none . . PASS Atlas-SNP SUN3 256979 hgsc.bcm.edu hg19 7 48035693 48035693 + Missense_Mutation SNP C C T novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . SUN3 NM_152782 exon8 c.G628A p.A210T ATTTTGCTTTATT . 126.0 40.0 115.0 0.0 . 52 . . . none . . PASS Atlas-SNP PEX1 5189 hgsc.bcm.edu hg19 7 92151473 92151473 + Silent SNP A A G novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . PEX1 NM_000466 exon2 c.T216C p.N72N AGCCACATTTTCA . 130.0 55.0 90.0 0.0 . 102 . . . none . . PASS Atlas-SNP TUSC3 7991 hgsc.bcm.edu hg19 8 15508312 15508312 + Missense_Mutation SNP G G A rs371225890 TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . TUSC3 NM_178234 exon3 c.G415A p.V139I ACAGACGTTTTTC . 222.0 96.0 163.0 0.0 . 98 . . . weak . . PASS Atlas-SNP PSD3 23362 hgsc.bcm.edu hg19 8 18430149 18430149 + Missense_Mutation SNP T T A novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . PSD3 NM_015310 exon14 c.A2673T p.K891N ATTGATTTTGTTT . 225.0 73.0 115.0 0.0 . 142 . . . none . . PASS Atlas-SNP ZNF395 55893 hgsc.bcm.edu hg19 8 28206721 28206721 + Missense_Mutation SNP T T C novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . ZNF395 NM_018660 exon9 c.A1351G p.S451G GCTCGCTGAAGCT . 70.0 22.0 110.0 0.0 . 54 . . . none . . PASS Atlas-SNP ARID3C 138715 hgsc.bcm.edu hg19 9 34622092 34622092 + Missense_Mutation SNP C C T novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . ARID3C NM_001017363 exon6 c.G1063A p.G355R GAGGCCCATCCAG . 130.0 44.0 184.0 0.0 . 33 . . . none . . PASS Atlas-SNP RUSC2 9853 hgsc.bcm.edu hg19 9 35547391 35547391 + Missense_Mutation SNP G G C novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . RUSC2 NM_014806 exon2 c.G873C p.M291I CAAGATGCATGGC . 93.0 31.0 150.0 0.0 . 88 . . . none . . PASS Atlas-SNP NANS 54187 hgsc.bcm.edu hg19 9 100840514 100840514 + Missense_Mutation SNP A A G novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . NANS NM_018946 exon4 c.A488G p.D163G CAATGGACACCAT . 127.0 47.0 167.0 0.0 . 24 . . . none . . PASS Atlas-SNP NR6A1 2649 hgsc.bcm.edu hg19 9 127316717 127316717 + Missense_Mutation SNP C C A novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . NR6A1 NM_033334 exon3 c.G275T p.R92L TATACCCGTTTGT . 135.0 7.0 107.0 0.0 . 38 . . . none . . PASS Atlas-SNP USP6NL 9712 hgsc.bcm.edu hg19 10 11523768 11523768 + Splice_Site SNP C C G novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 USP6NL,NS,carcinoma,0,1 USP6NL NM_014688 exon15 c.1078+1G>C . TTCTTACCAGGTT . 50.0 2.0 41.0 0.0 . 57 . . . none . . PASS Atlas-SNP THNSL1 79896 hgsc.bcm.edu hg19 10 25312238 25312238 + Missense_Mutation SNP C C T novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . THNSL1 NM_024838 exon3 c.C86T p.A29V AACATGCACAGCG . 118.0 48.0 80.0 0.0 . 70 . . . none . . PASS Atlas-SNP TULP3 7289 hgsc.bcm.edu hg19 12 3048537 3048537 + Missense_Mutation SNP A A C novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 .,1 TULP3 NM_003324 exon11 c.A1256C p.N419T ATTACAACTACCC . 165.0 48.0 170.0 0.0 . 45 . . . none . . PASS Atlas-SNP HEBP1 50865 hgsc.bcm.edu hg19 12 13142261 13142261 + Missense_Mutation SNP C C A novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . HEBP1 NM_015987 exon2 c.G167T p.R56L GCTTCCCGTAGAG . 138.0 7.0 118.0 0.0 . 16 . . . none . . PASS Atlas-SNP HOXC11 3227 hgsc.bcm.edu hg19 12 54367330 54367330 + Missense_Mutation SNP G G T novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 HOXC11_ENST00000546378,bladder,carcinoma,0,1 HOXC11 NM_014212 exon1 c.G305T p.R102L TGCACCGGGAGTG . 192.0 9.0 258.0 1.0 . 32 . . . none . . PASS Atlas-SNP ACAD10 80724 hgsc.bcm.edu hg19 12 112183962 112183962 + Silent SNP T T C novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . ACAD10 NM_001136538 exon15 c.T2223C p.A741A CAAAGCTGAAGGA . 101.0 34.0 132.0 0.0 . 93 . . . none . . PASS Atlas-SNP GAS6 2621 hgsc.bcm.edu hg19 13 114523928 114523928 + Missense_Mutation SNP T T C novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . GAS6 NM_000820 exon15 c.A1946G p.N649S CTCCGGTTGACCT . 52.0 23.0 69.0 0.0 . 75 . . . none . . PASS Atlas-SNP RBM23 55147 hgsc.bcm.edu hg19 14 23374814 23374814 + Splice_Site SNP C C G novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . RBM23 NM_018107 exon6 c.407+1G>C . AACCCACCTGACT . 40.0 26.0 99.0 0.0 . 44 . . . none . . PASS Atlas-SNP SMG1 23049 hgsc.bcm.edu hg19 16 18840922 18840922 + Missense_Mutation SNP G G T novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . SMG1 NM_015092 exon54 c.C9289A p.L3097I TGGGTAGCCCTAT . 70.0 40.0 38.0 0.0 . 401 . . . none . . PASS Atlas-SNP FTSJD1 55783 hgsc.bcm.edu hg19 16 71317552 71317552 + Missense_Mutation SNP C C T novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . FTSJD1 NM_018348 exon3 c.G2272A p.E758K CTCTCTCTCTTTG . 67.0 17.0 31.0 0.0 . 70 . . . none . . PASS Atlas-SNP PLCG2 5336 hgsc.bcm.edu hg19 16 81990321 81990321 + Missense_Mutation SNP T T G novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . PLCG2 NM_002661 exon32 c.T3592G p.S1198A CTTTACTCCTCCT . 77.0 28.0 67.0 0.0 . 276 . . . none . . PASS Atlas-SNP CRLF3 51379 hgsc.bcm.edu hg19 17 29119514 29119514 + Silent SNP C C A novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . CRLF3 NM_015986 exon6 c.G903T p.S301S AACACCCGATGAT . 189.0 11.0 205.0 0.0 . 36 . . . none . . PASS Atlas-SNP ZNHIT3 9326 hgsc.bcm.edu hg19 17 34849806 34849806 + Missense_Mutation SNP A A G novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . ZNHIT3 NM_004773 exon4 c.A242G p.D81G ATAGTGATGAGGA . 162.0 65.0 128.0 0.0 . 14 . . . none . . PASS Atlas-SNP DLX3 1747 hgsc.bcm.edu hg19 17 48072053 48072053 + Missense_Mutation SNP G G C novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . DLX3 NM_005220 exon1 c.C310G p.P104A GGGCTGGCAGCGG . 51.0 25.0 69.0 0.0 . 28 . . . none . . PASS Atlas-SNP TBCD 6904 hgsc.bcm.edu hg19 17 80885835 80885835 + Silent SNP G G C novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . TBCD NM_005993 exon30 c.G2664C p.R888R GGCTCGGAGCCAG . 97.0 33.0 108.0 0.0 . 94 . . . none . . PASS Atlas-SNP NPC1 4864 hgsc.bcm.edu hg19 18 21128030 21128030 + Missense_Mutation SNP G G T novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . NPC1 NM_000271 exon11 c.C1697A p.P566H TTGACAGGGAAGG . 184.0 72.0 207.0 0.0 . 114 . . . none . . PASS Atlas-SNP RNF165 494470 hgsc.bcm.edu hg19 18 44013357 44013357 + Missense_Mutation SNP A A G novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . RNF165 NM_152470 exon2 c.A266G p.Q89R CCCTGCAGTTCCA . 58.0 16.0 58.0 0.0 . 34 . . . none . . PASS Atlas-SNP ABCA7 10347 hgsc.bcm.edu hg19 19 1062293 1062293 + Missense_Mutation SNP C C A rs144378856 alternate_allele TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . ABCA7 NM_019112 exon42 c.C5693A p.P1898Q GTGTCCCGGAGGC . 128.0 8.0 244.0 0.0 . 174 . . . alt C|1.000;T|0.000 . PASS Atlas-SNP MUC16 94025 hgsc.bcm.edu hg19 19 9061598 9061598 + Silent SNP A A G novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . MUC16 NM_024690 exon3 c.T25848C p.P8616P ATTTGGAGGTGAA . 100.0 4.0 66.0 0.0 . 4315 . . . none . . PASS Atlas-SNP LDLR 3949 hgsc.bcm.edu hg19 19 11216253 11216253 + Missense_Mutation SNP A A C novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . LDLR NM_001195798 exon4 c.A671C p.D224A GCAAGGACAAATC . 66.0 28.0 74.0 0.0 . 72 . . . none . . PASS Atlas-SNP AP1M1 8907 hgsc.bcm.edu hg19 19 16339616 16339616 + Missense_Mutation SNP C C G novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . AP1M1 NM_001130524 exon10 c.C960G p.N320K AGCCAACAACGTG . 56.0 19.0 78.0 0.0 . 48 . . . none . . PASS Atlas-SNP ZNF737 100129842 hgsc.bcm.edu hg19 19 20728254 20728254 + Missense_Mutation SNP C C G novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 ZNF737,NS,carcinoma,0,1 ZNF737 NM_001159293 exon4 c.G755C p.S252T TCTCCACTATGAA . 33.0 2.0 22.0 0.0 . 50 . . . none . . PASS Atlas-SNP ZNF430 80264 hgsc.bcm.edu hg19 19 21240182 21240182 + Silent SNP A A G novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 ZNF430,NS,carcinoma,0,1 ZNF430 NM_025189 exon5 c.A1068G p.Q356Q TAACCAATCCTCA . 94.0 4.0 69.0 1.0 . 59 . . . none . . PASS Atlas-SNP FCGBP 8857 hgsc.bcm.edu hg19 19 40362919 40362919 + Missense_Mutation SNP C C A novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . FCGBP NM_003890 exon32 c.G15151T p.G5051W GCTGCCCGCAGGC . 82.0 8.0 148.0 0.0 . 416 . . . none . . PASS Atlas-SNP ZNF577 84765 hgsc.bcm.edu hg19 19 52376753 52376753 + Missense_Mutation SNP C C A rs200063901 by1000genomes;alternate_allele TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . ZNF577 NM_032679 exon7 c.G490T p.G164W CTCTCCCGCACAC . 159.0 7.0 158.0 0.0 . 63 . . . alt C|1.000;T|0.000 . PASS Atlas-SNP UBOX5 22888 hgsc.bcm.edu hg19 20 3102965 3102965 + Missense_Mutation SNP G G A novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . UBOX5 NM_014948 exon3 c.C320T p.P107L ACAGATGGCTCAG . 73.0 23.0 116.0 0.0 . 47 . . . none . . PASS Atlas-SNP PLAGL2 5326 hgsc.bcm.edu hg19 20 30784822 30784822 + Silent SNP C C A novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 PLAGL2,NS,carcinoma,-1,1 PLAGL2 NM_002657 exon3 c.G924T p.T308T CACGCCCGTGCTG . 146.0 8.0 177.0 1.0 . 56 . . . none . . PASS Atlas-SNP SETD4 54093 hgsc.bcm.edu hg19 21 37418117 37418117 + Silent SNP T T C novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . SETD4 NM_001007259 exon6 c.A489G p.R163R GTGGGCTCTCTGC . 204.0 90.0 200.0 0.0 . 37 . . . none . . PASS Atlas-SNP SIK1 150094 hgsc.bcm.edu hg19 21 44841223 44841223 + Missense_Mutation SNP T T C novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . SIK1 NM_173354 exon6 c.A524G p.K175R CCTGACTTGTAGA . 119.0 46.0 168.0 0.0 . 65 . . . none . . PASS Atlas-SNP COL18A1 80781 hgsc.bcm.edu hg19 21 46911142 46911142 + Missense_Mutation SNP G G A novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . COL18A1 NM_030582 exon21 c.G2611A p.D871N CAGGGAGATCCAG . 52.0 19.0 65.0 0.0 . 129 . . . none . . PASS Atlas-SNP COL18A1 80781 hgsc.bcm.edu hg19 21 46911143 46911143 + Missense_Mutation SNP A A T novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . COL18A1 NM_030582 exon21 c.A2612T p.D871V AGGGAGATCCAGG . 51.0 18.0 65.0 0.0 . 129 . . . none . . PASS Atlas-SNP PHF21B 112885 hgsc.bcm.edu hg19 22 45312440 45312440 + Missense_Mutation SNP G G T novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . PHF21B NM_138415 exon4 c.C284A p.P95H GTTGGGGGCTGCT . 85.0 30.0 134.0 0.0 . 61 . . . none . . PASS Atlas-SNP KLHL4 56062 hgsc.bcm.edu hg19 X 86773063 86773063 + Missense_Mutation SNP C C G novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . KLHL4 NM_019117 exon1 c.C167G p.S56C GCCACTCTCGGGA . 31.0 26.0 16.0 0.0 . 263 . . . none . . PASS Atlas-SNP GAB3 139716 hgsc.bcm.edu hg19 X 153928305 153928305 + Silent SNP G G T novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . GAB3 NM_001081573 exon5 c.C1099A p.R367R TGTCTCGGTGTCT . 137.0 7.0 84.0 0.0 . 73 . . . none . . PASS Atlas-SNP ND4 0 hgsc.bcm.edu hg19 MT 10816 10816 + Silent SNP A A G novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . . ENST00000361381 exon1 c.A57G p.K19K TTCCAAAAAACAC . 5.0 5.0 0.0 0.0 . . . . . none . . PASS Atlas-SNP HAO1 54363 hgsc.bcm.edu hg19 20 7886831 7886832 + In_Frame_Ins INS - - TTT novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . HAO1 NM_017545 exon4 c.691_692insAAA p.L231delinsKL . . 183.0 51.0 120.0 0.0 . 71 . 0.278689 0 none . . PASS Atlas-INDEL PROM1 8842 hgsc.bcm.edu hg19 4 15989284 15989287 + Frame_Shift_Del DEL ACCA ACCA - novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 ACCA ACCA . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . PROM1 NM_001145850 exon19 c.2130_2130del p.710_710del . . 233.0 69.0 228.0 0.0 . 91 . 0.296137 0 none . . PASS Atlas-INDEL BPIFB2 80341 hgsc.bcm.edu hg19 20 31604905 31604906 + Frame_Shift_Ins INS - - T novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . . NM_025227 exon7 c.574_575insT p.I192fs . . 111.0 35.0 143.0 0.0 . . . 0.315315 0 none . . PASS Atlas-INDEL RNF165 494470 hgsc.bcm.edu hg19 18 44013351 44013353 + In_Frame_Del DEL CCC CCC - novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 CCC CCC . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . RNF165 NM_152470 exon2 c.259_261del p.87_87del . . 49.0 15.0 51.0 0.0 . 34 . 0.306122 0 none . . PASS Atlas-INDEL SAMD4B 55095 hgsc.bcm.edu hg19 19 39868382 39868391 + Frame_Shift_Del DEL TCCCACTGAT TCCCACTGAT - novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 TCCCACTGAT TCCCACTGAT . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . SAMD4B NM_018028 exon10 c.1361_1370del p.454_457del . . 61.0 10.0 110.0 0.0 . 48 . 0.163934 0 none . . PASS Atlas-INDEL DOLK 22845 hgsc.bcm.edu hg19 9 131708944 131708945 + Frame_Shift_Ins INS - - G novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 . DOLK NM_014908 exon1 c.639_640insC p.L213fs . . 105.0 36.0 146.0 0.0 . 39 . 0.342857 0 none . . PASS Atlas-INDEL HDGF 3068 hgsc.bcm.edu hg19 1 156715103 156715104 + Frame_Shift_Ins INS - - A novel TCGA-A4-7583-01A-11D-2136-08 TCGA-A4-7583-10A-01D-2136-08 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b40c1178-c913-4b63-8863-f631473fffde 0a94c473-a646-42ca-9537-145517302063 .,2 HDGF NM_001126050 exon2 c.198_199insT p.F66fs . . 21.0 13.0 42.0 0.0 . 60 . 0.619048 0 none . . PASS Atlas-INDEL