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 dbSNP_AF Algorithm GPBP1L1 60313 hgsc.bcm.edu hg19 1 46124754 46124754 + Silent SNP C C A rs144406702 alternate_allele TCGA-BC-A69H-01A-11D-A30V-10 TCGA-BC-A69H-10A-01D-A30V-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b2e0f3c4-dcff-4718-8461-381609521e4f 371b4d98-49a4-4605-a24e-d7b92923da58 GPBP1L1,colon,carcinoma,0,1 GPBP1L1 NM_021639 exon4 c.G6T p.A2A ATGCTGCGCCATT . 51.0 3.0 112.0 0.0 . 43 . C|1.000;T|0.000 Atlas-SNP INSRR 3645 hgsc.bcm.edu hg19 1 156815550 156815550 + Missense_Mutation SNP G G T novel TCGA-BC-A69H-01A-11D-A30V-10 TCGA-BC-A69H-10A-01D-A30V-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b2e0f3c4-dcff-4718-8461-381609521e4f 371b4d98-49a4-4605-a24e-d7b92923da58 . INSRR NM_014215 exon10 c.C2035A p.P679T CCTCAGGATCCCC . 81.0 4.0 76.0 0.0 . 309 . . Atlas-SNP POU2F1 5451 hgsc.bcm.edu hg19 1 167384897 167384897 + Silent SNP T T C novel TCGA-BC-A69H-01A-11D-A30V-10 TCGA-BC-A69H-10A-01D-A30V-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b2e0f3c4-dcff-4718-8461-381609521e4f 371b4d98-49a4-4605-a24e-d7b92923da58 . POU2F1 NM_002697 exon16 c.T2151C p.S717S GGTCTCTGCCGCC . 80.0 21.0 133.0 0.0 . 120 . . Atlas-SNP PKP1 5317 hgsc.bcm.edu hg19 1 201294914 201294914 + Missense_Mutation SNP T T C novel TCGA-BC-A69H-01A-11D-A30V-10 TCGA-BC-A69H-10A-01D-A30V-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b2e0f3c4-dcff-4718-8461-381609521e4f 371b4d98-49a4-4605-a24e-d7b92923da58 . PKP1 NM_000299 exon13 c.T2117C p.L706P CCCGGCTTCTCCT . 116.0 25.0 139.0 0.0 . 127 . . Atlas-SNP USH2A 7399 hgsc.bcm.edu hg19 1 215802343 215802343 + Missense_Mutation SNP G G A novel TCGA-BC-A69H-01A-11D-A30V-10 TCGA-BC-A69H-10A-01D-A30V-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b2e0f3c4-dcff-4718-8461-381609521e4f 371b4d98-49a4-4605-a24e-d7b92923da58 . USH2A NM_206933 exon71 c.C15332T p.T5111I ACAGGTGTCCCAG . 109.0 13.0 164.0 0.0 . 1168 . . Atlas-SNP AMMECR1L 83607 hgsc.bcm.edu hg19 2 128628831 128628831 + Silent SNP C C T novel TCGA-BC-A69H-01A-11D-A30V-10 TCGA-BC-A69H-10A-01D-A30V-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b2e0f3c4-dcff-4718-8461-381609521e4f 371b4d98-49a4-4605-a24e-d7b92923da58 . AMMECR1L NM_031445 exon4 c.G510A p.T170T GGTTAACGTGTAT . 44.0 10.0 74.0 0.0 . 22 . . Atlas-SNP IL5RA 3568 hgsc.bcm.edu hg19 3 3137002 3137002 + Missense_Mutation SNP G G T novel TCGA-BC-A69H-01A-11D-A30V-10 TCGA-BC-A69H-10A-01D-A30V-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b2e0f3c4-dcff-4718-8461-381609521e4f 371b4d98-49a4-4605-a24e-d7b92923da58 . IL5RA NM_001243099 exon8 c.C836A p.T279K TTCCTTGTATTGT . 116.0 51.0 161.0 0.0 . 55 . . Atlas-SNP ATP2B2 491 hgsc.bcm.edu hg19 3 10417206 10417206 + Missense_Mutation SNP T T C novel TCGA-BC-A69H-01A-11D-A30V-10 TCGA-BC-A69H-10A-01D-A30V-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b2e0f3c4-dcff-4718-8461-381609521e4f 371b4d98-49a4-4605-a24e-d7b92923da58 . ATP2B2 NM_001001331 exon11 c.A1324G p.K442E AGAACTTGACAAA . 126.0 13.0 135.0 0.0 . 304 . . Atlas-SNP PXK 54899 hgsc.bcm.edu hg19 3 58395296 58395296 + Missense_Mutation SNP A A G novel TCGA-BC-A69H-01A-11D-A30V-10 TCGA-BC-A69H-10A-01D-A30V-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b2e0f3c4-dcff-4718-8461-381609521e4f 371b4d98-49a4-4605-a24e-d7b92923da58 . PXK NM_017771 exon15 c.A1346G p.H449R AGTCCCACCATGG . 196.0 93.0 253.0 1.0 . 89 . . Atlas-SNP FGFR3 2261 hgsc.bcm.edu hg19 4 1807577 1807577 + Silent SNP C C T novel TCGA-BC-A69H-01A-11D-A30V-10 TCGA-BC-A69H-10A-01D-A30V-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b2e0f3c4-dcff-4718-8461-381609521e4f 371b4d98-49a4-4605-a24e-d7b92923da58 . FGFR3 NM_001163213 exon13 c.C1752T p.C584C CACCTGCAAGCCG . 54.0 16.0 76.0 0.0 . 3320 . . Atlas-SNP SH3BP2 6452 hgsc.bcm.edu hg19 4 2829348 2829348 + Missense_Mutation SNP A A G novel TCGA-BC-A69H-01A-11D-A30V-10 TCGA-BC-A69H-10A-01D-A30V-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b2e0f3c4-dcff-4718-8461-381609521e4f 371b4d98-49a4-4605-a24e-d7b92923da58 . SH3BP2 NM_001145856 exon7 c.A704G p.D235G ACGACGATGAGGA . 67.0 30.0 127.0 0.0 . 43 . . Atlas-SNP FHDC1 85462 hgsc.bcm.edu hg19 4 153896514 153896514 + Nonsense_Mutation SNP G G T novel TCGA-BC-A69H-01A-11D-A30V-10 TCGA-BC-A69H-10A-01D-A30V-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b2e0f3c4-dcff-4718-8461-381609521e4f 371b4d98-49a4-4605-a24e-d7b92923da58 . FHDC1 NM_033393 exon11 c.G2071T p.E691X GGCATGGAGGAGA . 29.0 12.0 71.0 0.0 . 102 . . Atlas-SNP CYFIP2 26999 hgsc.bcm.edu hg19 5 156712348 156712348 + Splice_Site SNP G G T novel TCGA-BC-A69H-01A-11D-A30V-10 TCGA-BC-A69H-10A-01D-A30V-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b2e0f3c4-dcff-4718-8461-381609521e4f 371b4d98-49a4-4605-a24e-d7b92923da58 . CYFIP2 . . . . CCTTCAGTGCAGA . 39.0 6.0 39.0 0.0 . 354 . . Atlas-SNP CCNJL 79616 hgsc.bcm.edu hg19 5 159686508 159686508 + Missense_Mutation SNP T T G novel TCGA-BC-A69H-01A-11D-A30V-10 TCGA-BC-A69H-10A-01D-A30V-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b2e0f3c4-dcff-4718-8461-381609521e4f 371b4d98-49a4-4605-a24e-d7b92923da58 . CCNJL NM_024565 exon5 c.A695C p.Y232S TGGGCATACTCCT . 31.0 7.0 48.0 0.0 . 36 . . Atlas-SNP EYS 346007 hgsc.bcm.edu hg19 6 65612320 65612320 + Silent SNP A A G novel TCGA-BC-A69H-01A-11D-A30V-10 TCGA-BC-A69H-10A-01D-A30V-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b2e0f3c4-dcff-4718-8461-381609521e4f 371b4d98-49a4-4605-a24e-d7b92923da58 . EYS NM_001142800 exon17 c.T2715C p.C905C ATCTTCACAGTCA . 121.0 26.0 203.0 0.0 . 527 . . Atlas-SNP CSMD1 64478 hgsc.bcm.edu hg19 8 3165845 3165845 + Missense_Mutation SNP G G T novel TCGA-BC-A69H-01A-11D-A30V-10 TCGA-BC-A69H-10A-01D-A30V-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b2e0f3c4-dcff-4718-8461-381609521e4f 371b4d98-49a4-4605-a24e-d7b92923da58 . CSMD1 NM_033225 exon24 c.C3812A p.P1271H CACGAAGGTAGTG . 22.0 4.0 71.0 0.0 . 1469 . . Atlas-SNP MTMR7 9108 hgsc.bcm.edu hg19 8 17163407 17163407 + Missense_Mutation SNP T T G novel TCGA-BC-A69H-01A-11D-A30V-10 TCGA-BC-A69H-10A-01D-A30V-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b2e0f3c4-dcff-4718-8461-381609521e4f 371b4d98-49a4-4605-a24e-d7b92923da58 . MTMR7 NM_004686 exon11 c.A1211C p.E404A ACACACTCAATGA . 33.0 14.0 142.0 0.0 . 75 . . Atlas-SNP RFX3 5991 hgsc.bcm.edu hg19 9 3247979 3247979 + Missense_Mutation SNP T T A novel TCGA-BC-A69H-01A-11D-A30V-10 TCGA-BC-A69H-10A-01D-A30V-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b2e0f3c4-dcff-4718-8461-381609521e4f 371b4d98-49a4-4605-a24e-d7b92923da58 . RFX3 NM_002919 exon16 c.A2021T p.E674V TGTAATTCTGGCT . 32.0 12.0 66.0 0.0 . 156 . . Atlas-SNP PLAA 9373 hgsc.bcm.edu hg19 9 26905887 26905887 + Missense_Mutation SNP C C G novel TCGA-BC-A69H-01A-11D-A30V-10 TCGA-BC-A69H-10A-01D-A30V-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b2e0f3c4-dcff-4718-8461-381609521e4f 371b4d98-49a4-4605-a24e-d7b92923da58 . PLAA NM_001031689 exon14 c.G2010C p.Q670H TCCTGCCTGGCCA . 93.0 22.0 198.0 0.0 . 48 . . Atlas-SNP GRIN3A 116443 hgsc.bcm.edu hg19 9 104499796 104499796 + Missense_Mutation SNP C C G novel TCGA-BC-A69H-01A-11D-A30V-10 TCGA-BC-A69H-10A-01D-A30V-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b2e0f3c4-dcff-4718-8461-381609521e4f 371b4d98-49a4-4605-a24e-d7b92923da58 . GRIN3A NM_133445 exon1 c.G466C p.A156P GGCCTGCCTCGAT . 54.0 19.0 108.0 0.0 . 186 . . Atlas-SNP TMEM38B 55151 hgsc.bcm.edu hg19 9 108536210 108536210 + Nonsense_Mutation SNP G G A novel TCGA-BC-A69H-01A-11D-A30V-10 TCGA-BC-A69H-10A-01D-A30V-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b2e0f3c4-dcff-4718-8461-381609521e4f 371b4d98-49a4-4605-a24e-d7b92923da58 . TMEM38B NM_018112 exon6 c.G725A p.W242X TGAGTTGGATGCT . 95.0 34.0 158.0 0.0 . 31 . . Atlas-SNP SVEP1 79987 hgsc.bcm.edu hg19 9 113312149 113312149 + Missense_Mutation SNP G G C novel TCGA-BC-A69H-01A-11D-A30V-10 TCGA-BC-A69H-10A-01D-A30V-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b2e0f3c4-dcff-4718-8461-381609521e4f 371b4d98-49a4-4605-a24e-d7b92923da58 . SVEP1 NM_153366 exon2 c.C767G p.A256G CGGCGAGCTAAAG . 83.0 16.0 171.0 0.0 . 326 . . Atlas-SNP FAM78A 286336 hgsc.bcm.edu hg19 9 134136583 134136583 + Missense_Mutation SNP C C T novel TCGA-BC-A69H-01A-11D-A30V-10 TCGA-BC-A69H-10A-01D-A30V-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b2e0f3c4-dcff-4718-8461-381609521e4f 371b4d98-49a4-4605-a24e-d7b92923da58 . FAM78A NM_033387 exon2 c.G478A p.D160N AGTTGTCATTCAT . 30.0 7.0 57.0 0.0 . 28 . . Atlas-SNP RET 5979 hgsc.bcm.edu hg19 10 43600449 43600449 + Silent SNP G G A novel TCGA-BC-A69H-01A-11D-A30V-10 TCGA-BC-A69H-10A-01D-A30V-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b2e0f3c4-dcff-4718-8461-381609521e4f 371b4d98-49a4-4605-a24e-d7b92923da58 . RET NM_020630 exon4 c.G675A p.T225T GAGCACGCGCTGG . 40.0 13.0 59.0 0.0 . 916 . . Atlas-SNP RBP3 5949 hgsc.bcm.edu hg19 10 48389747 48389747 + Silent SNP C C T novel TCGA-BC-A69H-01A-11D-A30V-10 TCGA-BC-A69H-10A-01D-A30V-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b2e0f3c4-dcff-4718-8461-381609521e4f 371b4d98-49a4-4605-a24e-d7b92923da58 . RBP3 NM_002900 exon1 c.G1131A p.Q377Q CGCAGCCTGCAGG . 41.0 15.0 57.0 0.0 . 152 . . Atlas-SNP CTSD 1509 hgsc.bcm.edu hg19 11 1778644 1778644 + Missense_Mutation SNP C C T rs371522391 TCGA-BC-A69H-01A-11D-A30V-10 TCGA-BC-A69H-10A-01D-A30V-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b2e0f3c4-dcff-4718-8461-381609521e4f 371b4d98-49a4-4605-a24e-d7b92923da58 . CTSD NM_001909 exon5 c.G614A p.R205H GAGATGCGGGGGT . 68.0 34.0 61.0 0.0 . 26 . . Atlas-SNP OR52N4 390072 hgsc.bcm.edu hg19 11 5776243 5776243 + Silent SNP C C G novel TCGA-BC-A69H-01A-11D-A30V-10 TCGA-BC-A69H-10A-01D-A30V-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b2e0f3c4-dcff-4718-8461-381609521e4f 371b4d98-49a4-4605-a24e-d7b92923da58 OR52N4,right_upper_lobe,carcinoma,0,1 OR52N4 NM_001005175 exon1 c.C273G p.L91L TCATCTCAAGGAC . 74.0 12.0 123.0 0.0 . 55 . . Atlas-SNP NRXN2 9379 hgsc.bcm.edu hg19 11 64434901 64434901 + Missense_Mutation SNP C C A rs143130600 bycluster;by1000genomes;alternate_allele TCGA-BC-A69H-01A-11D-A30V-10 TCGA-BC-A69H-10A-01D-A30V-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b2e0f3c4-dcff-4718-8461-381609521e4f 371b4d98-49a4-4605-a24e-d7b92923da58 . NRXN2 NM_015080 exon9 c.G1619T p.G540V GCTCCACCCCCAG . 49.0 11.0 81.0 0.0 . 247 . C|1.000;T|0.000 Atlas-SNP NLRX1 79671 hgsc.bcm.edu hg19 11 119052990 119052990 + Missense_Mutation SNP G G A novel TCGA-BC-A69H-01A-11D-A30V-10 TCGA-BC-A69H-10A-01D-A30V-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b2e0f3c4-dcff-4718-8461-381609521e4f 371b4d98-49a4-4605-a24e-d7b92923da58 . NLRX1 NM_024618 exon9 c.G2542A p.G848S GGTGCTGGTGACA . 25.0 7.0 56.0 0.0 . 128 . . Atlas-SNP EEA1 8411 hgsc.bcm.edu hg19 12 93205205 93205205 + Silent SNP T T C novel TCGA-BC-A69H-01A-11D-A30V-10 TCGA-BC-A69H-10A-01D-A30V-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b2e0f3c4-dcff-4718-8461-381609521e4f 371b4d98-49a4-4605-a24e-d7b92923da58 . EEA1 NM_003566 exon17 c.A2049G p.L683L CTTATTTAACTCC . 43.0 11.0 48.0 0.0 . 104 . . Atlas-SNP MAP4K5 11183 hgsc.bcm.edu hg19 14 50911780 50911780 + Missense_Mutation SNP C C A novel TCGA-BC-A69H-01A-11D-A30V-10 TCGA-BC-A69H-10A-01D-A30V-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b2e0f3c4-dcff-4718-8461-381609521e4f 371b4d98-49a4-4605-a24e-d7b92923da58 . MAP4K5 NM_006575 exon18 c.G1318T p.V440L CTGCCACAGGCCC . 73.0 16.0 122.0 0.0 . 48 . . Atlas-SNP CYLD 1540 hgsc.bcm.edu hg19 16 50815217 50815217 + Missense_Mutation SNP G G A novel TCGA-BC-A69H-01A-11D-A30V-10 TCGA-BC-A69H-10A-01D-A30V-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b2e0f3c4-dcff-4718-8461-381609521e4f 371b4d98-49a4-4605-a24e-d7b92923da58 . CYLD NM_015247 exon11 c.G1579A p.A527T ACCTGTGCCCTGA . 55.0 17.0 105.0 0.0 . 150 . . Atlas-SNP TAF1C 9013 hgsc.bcm.edu hg19 16 84214736 84214736 + Missense_Mutation SNP C C A novel TCGA-BC-A69H-01A-11D-A30V-10 TCGA-BC-A69H-10A-01D-A30V-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b2e0f3c4-dcff-4718-8461-381609521e4f 371b4d98-49a4-4605-a24e-d7b92923da58 . TAF1C NM_005679 exon11 c.G1299T p.Q433H CCCTTTCTGGCAC . 54.0 28.0 114.0 0.0 . 60 . . Atlas-SNP FASN 2194 hgsc.bcm.edu hg19 17 80051623 80051623 + Missense_Mutation SNP C C T novel TCGA-BC-A69H-01A-11D-A30V-10 TCGA-BC-A69H-10A-01D-A30V-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b2e0f3c4-dcff-4718-8461-381609521e4f 371b4d98-49a4-4605-a24e-d7b92923da58 . FASN NM_004104 exon4 c.G305A p.G102E TGTGTTCCTCGGA . 68.0 40.0 45.0 0.0 . 154 . . Atlas-SNP FOXK2 3607 hgsc.bcm.edu hg19 17 80477826 80477826 + Missense_Mutation SNP G G C novel TCGA-BC-A69H-01A-11D-A30V-10 TCGA-BC-A69H-10A-01D-A30V-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b2e0f3c4-dcff-4718-8461-381609521e4f 371b4d98-49a4-4605-a24e-d7b92923da58 FOXK2,NS,carcinoma,0,1 FOXK2 NM_004514 exon1 c.G62C p.G21A GGGCCGGGGGCGG . 4.0 2.0 1.0 0.0 . 46 . . Atlas-SNP LAMA1 284217 hgsc.bcm.edu hg19 18 7002349 7002349 + Silent SNP A A G novel TCGA-BC-A69H-01A-11D-A30V-10 TCGA-BC-A69H-10A-01D-A30V-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b2e0f3c4-dcff-4718-8461-381609521e4f 371b4d98-49a4-4605-a24e-d7b92923da58 . LAMA1 NM_005559 exon30 c.T4296C p.D1432D ACACACATCACAA . 37.0 9.0 52.0 0.0 . 458 . . Atlas-SNP CPAMD8 27151 hgsc.bcm.edu hg19 19 17040002 17040002 + Missense_Mutation SNP T T A novel TCGA-BC-A69H-01A-11D-A30V-10 TCGA-BC-A69H-10A-01D-A30V-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b2e0f3c4-dcff-4718-8461-381609521e4f 371b4d98-49a4-4605-a24e-d7b92923da58 . CPAMD8 NM_015692 exon24 c.A3035T p.Q1012L GGCCGCTGCACAT . 30.0 5.0 37.0 0.0 . 192 . . Atlas-SNP CILP2 148113 hgsc.bcm.edu hg19 19 19655201 19655201 + Missense_Mutation SNP C C A novel TCGA-BC-A69H-01A-11D-A30V-10 TCGA-BC-A69H-10A-01D-A30V-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b2e0f3c4-dcff-4718-8461-381609521e4f 371b4d98-49a4-4605-a24e-d7b92923da58 . CILP2 NM_153221 exon8 c.C1847A p.T616N ACCTCACCTCGGC . 41.0 17.0 71.0 0.0 . 84 . . Atlas-SNP RBM42 79171 hgsc.bcm.edu hg19 19 36120133 36120133 + Silent SNP G G T rs371589146 alternate_allele TCGA-BC-A69H-01A-11D-A30V-10 TCGA-BC-A69H-10A-01D-A30V-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b2e0f3c4-dcff-4718-8461-381609521e4f 371b4d98-49a4-4605-a24e-d7b92923da58 . RBM42 NM_024321 exon1 c.G78T p.P26P CATCCCGGGCAAA . 27.0 11.0 35.0 0.0 . 40 . . Atlas-SNP ZBTB32 27033 hgsc.bcm.edu hg19 19 36207170 36207170 + Missense_Mutation SNP A A T novel TCGA-BC-A69H-01A-11D-A30V-10 TCGA-BC-A69H-10A-01D-A30V-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b2e0f3c4-dcff-4718-8461-381609521e4f 371b4d98-49a4-4605-a24e-d7b92923da58 . ZBTB32 NM_014383 exon5 c.A1160T p.Q387L AGCATCAGATGGA . 81.0 27.0 82.0 0.0 . 33 . . Atlas-SNP PTOV1 53635 hgsc.bcm.edu hg19 19 50361895 50361895 + Silent SNP C C A rs376020024 TCGA-BC-A69H-01A-11D-A30V-10 TCGA-BC-A69H-10A-01D-A30V-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b2e0f3c4-dcff-4718-8461-381609521e4f 371b4d98-49a4-4605-a24e-d7b92923da58 . PTOV1 NM_017432 exon10 c.C1026A p.I342I CCGGATCATGGAC . 52.0 25.0 81.0 0.0 . 41 . . Atlas-SNP SYNDIG1 79953 hgsc.bcm.edu hg19 20 24565510 24565510 + Missense_Mutation SNP A A G novel TCGA-BC-A69H-01A-11D-A30V-10 TCGA-BC-A69H-10A-01D-A30V-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b2e0f3c4-dcff-4718-8461-381609521e4f 371b4d98-49a4-4605-a24e-d7b92923da58 SYNDIG1,NS,carcinoma,0,1 SYNDIG1 NM_024893 exon3 c.A499G p.T167A AGCGACACAGAGA . 64.0 29.0 60.0 1.0 . 58 . . Atlas-SNP DSCAM 1826 hgsc.bcm.edu hg19 21 42080424 42080424 + Missense_Mutation SNP T T A novel TCGA-BC-A69H-01A-11D-A30V-10 TCGA-BC-A69H-10A-01D-A30V-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b2e0f3c4-dcff-4718-8461-381609521e4f 371b4d98-49a4-4605-a24e-d7b92923da58 . DSCAM NM_001271534 exon2 c.A317T p.N106I GAAGGATTTTCAG . 46.0 15.0 69.0 0.0 . 347 . . Atlas-SNP SIK1 150094 hgsc.bcm.edu hg19 21 44841639 44841639 + Silent SNP C C T novel TCGA-BC-A69H-01A-11D-A30V-10 TCGA-BC-A69H-10A-01D-A30V-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b2e0f3c4-dcff-4718-8461-381609521e4f 371b4d98-49a4-4605-a24e-d7b92923da58 SIK1,caecum,carcinoma,0,1 SIK1 NM_173354 exon5 c.G378A p.A126A CTTCCGCGCCTCG . 78.0 24.0 111.0 0.0 . 65 . . Atlas-SNP SHROOM4 57477 hgsc.bcm.edu hg19 X 50350826 50350826 + Missense_Mutation SNP G G T novel TCGA-BC-A69H-01A-11D-A30V-10 TCGA-BC-A69H-10A-01D-A30V-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b2e0f3c4-dcff-4718-8461-381609521e4f 371b4d98-49a4-4605-a24e-d7b92923da58 . SHROOM4 NM_020717 exon6 c.C3316A p.P1106T TGGGAGGAGGAGG . 30.0 17.0 92.0 0.0 . 171 . . Atlas-SNP PABPC5 140886 hgsc.bcm.edu hg19 X 90690699 90690699 + Silent SNP T T A novel TCGA-BC-A69H-01A-11D-A30V-10 TCGA-BC-A69H-10A-01D-A30V-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b2e0f3c4-dcff-4718-8461-381609521e4f 371b4d98-49a4-4605-a24e-d7b92923da58 . PABPC5 NM_080832 exon2 c.T123A p.A41A GCCTGCTGGCCCT . 16.0 10.0 53.0 0.0 . 92 . . Atlas-SNP GLRA4 441509 hgsc.bcm.edu hg19 X 102978843 102978843 + Missense_Mutation SNP A A C novel TCGA-BC-A69H-01A-11D-A30V-10 TCGA-BC-A69H-10A-01D-A30V-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b2e0f3c4-dcff-4718-8461-381609521e4f 371b4d98-49a4-4605-a24e-d7b92923da58 . GLRA4 NM_001024452 exon5 c.T518G p.L173R TCCATCAGGCAGG . 102.0 69.0 280.0 1.0 . 86 . . Atlas-SNP RAB9B 51209 hgsc.bcm.edu hg19 X 103080318 103080318 + Missense_Mutation SNP C C T novel TCGA-BC-A69H-01A-11D-A30V-10 TCGA-BC-A69H-10A-01D-A30V-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b2e0f3c4-dcff-4718-8461-381609521e4f 371b4d98-49a4-4605-a24e-d7b92923da58 . RAB9B NM_016370 exon3 c.G397A p.V133M TAGTCACTTGCCT . 24.0 17.0 91.0 0.0 . 24 . . Atlas-SNP HGS 9146 hgsc.bcm.edu hg19 17 79660939 79660939 + Frame_Shift_Del DEL C C - novel TCGA-BC-A69H-01A-11D-A30V-10 TCGA-BC-A69H-10A-01D-A30V-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b2e0f3c4-dcff-4718-8461-381609521e4f 371b4d98-49a4-4605-a24e-d7b92923da58 . HGS NM_004712 exon11 c.879delG p.E293fs . . 54.0 15.0 28.0 0.0 . 54 . . Atlas-Indel,Pindel TP53 7157 hgsc.bcm.edu hg19 17 7579389 7579399 + Frame_Shift_Del DEL GGGAAGGGACA GGGAAGGGACA - novel TCGA-BC-A69H-01A-11D-A30V-10 TCGA-BC-A69H-10A-01D-A30V-10 GGGAAGGGACA GGGAAGGGACA . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b2e0f3c4-dcff-4718-8461-381609521e4f 371b4d98-49a4-4605-a24e-d7b92923da58 . TP53 NM_001126112 exon4 c.289_299del p.97_100del . . 64.0 23.0 190.0 0.0 . 33396 . . Atlas-Indel,Pindel SUN5 140732 hgsc.bcm.edu hg19 20 31577506 31577506 + Splice_Site DEL T T - novel TCGA-BC-A69H-01A-11D-A30V-10 TCGA-BC-A69H-10A-01D-A30V-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b2e0f3c4-dcff-4718-8461-381609521e4f 371b4d98-49a4-4605-a24e-d7b92923da58 . SUN5 NM_080675 exon10 c.535-1A>- . . . 66.0 18.0 79.0 0.0 . 63 . . Pindel MSN 4478 hgsc.bcm.edu hg19 X 64951035 64951044 + Frame_Shift_Del DEL ACACCGTGGC ACACCGTGGC - novel TCGA-BC-A69H-01A-11D-A30V-10 TCGA-BC-A69H-10A-01D-A30V-10 ACACCGTGGC ACACCGTGGC . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq b2e0f3c4-dcff-4718-8461-381609521e4f 371b4d98-49a4-4605-a24e-d7b92923da58 . MSN NM_002444 exon5 c.533_542del p.178_181del . . 56.0 17.0 154.0 0.0 . 89 . . Pindel