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 MTOR 2475 hgsc.bcm.edu hg19 1 11273603 11273603 + Silent SNP G G C novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . MTOR NM_004958 exon21 c.C3138G p.T1046T AATTGAGGTGTTC . 187.0 71.0 129.0 0.0 . 327 . . . none . . PASS Atlas-SNP UBR4 23352 hgsc.bcm.edu hg19 1 19490300 19490300 + Missense_Mutation SNP C C G novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . UBR4 NM_020765 exon34 c.G4722C p.K1574N TACATTCTTCTGT . 175.0 70.0 214.0 0.0 . 415 . . . none . . PASS Atlas-SNP EPHA8 2046 hgsc.bcm.edu hg19 1 22927186 22927186 + Silent SNP A A T novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . EPHA8 NM_020526 exon14 c.A2421T p.P807P GGCCCCAGAGGCC . 225.0 82.0 249.0 0.0 . 221 . . . none . . PASS Atlas-SNP MCOLN3 55283 hgsc.bcm.edu hg19 1 85487988 85487988 + Missense_Mutation SNP C C A novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . MCOLN3 NM_018298 exon10 c.G1191T p.K397N GTTGTACTTTGCA . 52.0 19.0 27.0 0.0 . 74 . . . none . . PASS Atlas-SNP CD46 4179 hgsc.bcm.edu hg19 1 207940508 207940508 + Missense_Mutation SNP C C A novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . CD46 NM_172352 exon6 c.C824A p.T275N ACAGTACTTGGGA . 60.0 23.0 80.0 0.0 . 34 . . . none . . PASS Atlas-SNP RBM34 23029 hgsc.bcm.edu hg19 1 235318245 235318245 + Missense_Mutation SNP T T A novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . RBM34 NM_001161533 exon4 c.A548T p.N183I CTCTCATTCTTTA . 266.0 90.0 288.0 0.0 . 41 . . . none . . PASS Atlas-SNP HADHA 3030 hgsc.bcm.edu hg19 2 26459821 26459821 + Missense_Mutation SNP G G C novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . HADHA NM_000182 exon4 c.C216G p.F72L TTCTGAGAACTCT . 246.0 82.0 180.0 0.0 . 87 . . . none . . PASS Atlas-SNP GTF3C2 2976 hgsc.bcm.edu hg19 2 27565920 27565920 + Silent SNP G G T novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . GTF3C2 NM_001521 exon4 c.T342A p.V114V CTGTTGGGGCCTT . 227.0 78.0 331.0 1.0 . 73 . . . none . . PASS Atlas-SNP HAAO 23498 hgsc.bcm.edu hg19 2 42994588 42994588 + Missense_Mutation SNP G G C novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . HAAO NM_012205 exon10 c.C850G p.P284A CCAGGGGCTTCTT . 67.0 11.0 61.0 0.0 . 26 . . . none . . PASS Atlas-SNP BIN1 274 hgsc.bcm.edu hg19 2 127818193 127818193 + Missense_Mutation SNP C C G rs117721706 bycluster;byfrequency;by1000genomes;alternate_allele TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . BIN1 NM_139346 exon10 c.G788C p.R263P CGCAGCCGCGAAA . 143.0 47.0 183.0 0.0 . 85 . . . alt C|0.992;T|0.008 . PASS Atlas-SNP TRNT1 51095 hgsc.bcm.edu hg19 3 3189651 3189651 + Missense_Mutation SNP G G C novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . TRNT1 NM_182916 exon8 c.G1118C p.C373S AGCACTGTCTCCT . 20.0 8.0 38.0 0.0 . 34 . . . none . . PASS Atlas-SNP OSBPL10 114884 hgsc.bcm.edu hg19 3 31774841 31774841 + Missense_Mutation SNP G G A novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . OSBPL10 NM_017784 exon6 c.C1003T p.L335F AGCCAAGTGTCCC . 285.0 80.0 318.0 0.0 . 160 . . . none . . PASS Atlas-SNP ATR 545 hgsc.bcm.edu hg19 3 142274792 142274792 + Silent SNP A A T novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . ATR NM_001184 exon10 c.T2268A p.S756S TAGTTGAGAAGAT . 128.0 42.0 178.0 0.0 . 285 . . . none . . PASS Atlas-SNP SLC26A1 10861 hgsc.bcm.edu hg19 4 985220 985220 + Missense_Mutation SNP G G A novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . SLC26A1 NM_022042 exon2 c.C272T p.S91L AGCAATGAGTAGG . 228.0 82.0 257.0 0.0 . 44 . . . none . . PASS Atlas-SNP ACOX3 8310 hgsc.bcm.edu hg19 4 8417674 8417674 + Missense_Mutation SNP C C T novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . ACOX3 NM_001101667 exon3 c.G197A p.G66E TCGGCTCCAGGGG . 197.0 74.0 231.0 0.0 . 70 . . . none . . PASS Atlas-SNP AASDH 132949 hgsc.bcm.edu hg19 4 57248668 57248668 + Missense_Mutation SNP A A T novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . AASDH NM_181806 exon3 c.T326A p.I109N ACAAGGATATACT . 45.0 16.0 72.0 0.0 . 101 . . . none . . PASS Atlas-SNP ABCG2 9429 hgsc.bcm.edu hg19 4 89039327 89039327 + Silent SNP A A G novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . ABCG2 NM_004827 exon7 c.T775C p.L259L AGGCCAATAAGGT . 86.0 32.0 99.0 0.0 . 151 . . . none . . PASS Atlas-SNP NDST4 64579 hgsc.bcm.edu hg19 4 115767018 115767018 + Silent SNP G G A novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . NDST4 NM_022569 exon10 c.C2076T p.I692I AATGAGGATGGTG . 128.0 51.0 135.0 0.0 . 193 . . . none . . PASS Atlas-SNP ASB5 140458 hgsc.bcm.edu hg19 4 177136796 177136796 + Silent SNP T T C novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . ASB5 NM_080874 exon7 c.A945G p.Q315Q CTGGAGTTGTGGG . 56.0 16.0 68.0 0.0 . 88 . . . none . . PASS Atlas-SNP FAM149A 25854 hgsc.bcm.edu hg19 4 187077186 187077186 + Missense_Mutation SNP A A G novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . FAM149A NM_001006655 exon6 c.A416G p.Q139R CAGCTCAGCCCGG . 114.0 41.0 132.0 0.0 . 52 . . . none . . PASS Atlas-SNP LIFR 3977 hgsc.bcm.edu hg19 5 38504185 38504185 + Missense_Mutation SNP T T C novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . LIFR NM_002310 exon10 c.A1330G p.I444V AATTAATATCCTT . 57.0 18.0 66.0 0.0 . 348 . . . none . . PASS Atlas-SNP SLC36A3 285641 hgsc.bcm.edu hg19 5 150660717 150660717 + Nonsense_Mutation SNP G G T novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . SLC36A3 NM_001145017 exon10 c.C1125A p.Y375X GATAGAGTACATC . 198.0 75.0 186.0 0.0 . 54 . . . none . . PASS Atlas-SNP RGS14 10636 hgsc.bcm.edu hg19 5 176797996 176797996 + Missense_Mutation SNP G G T novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . RGS14 NM_006480 exon11 c.G1218T p.K406N GGAGAAGCACGGC . 49.0 16.0 72.0 0.0 . 34 . . . none . . PASS Atlas-SNP OR11A1 26531 hgsc.bcm.edu hg19 6 29395381 29395381 + Missense_Mutation SNP T T G novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . OR11A1 NM_013937 exon1 c.A38C p.E13A ACAAATTCAGTAA . 98.0 34.0 130.0 0.0 . 30 . . . none . . PASS Atlas-SNP SEPT7 989 hgsc.bcm.edu hg19 7 35912377 35912377 + Splice_Site SNP G G A novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . SEPT7 NM_001011553 exon4 c.374+1G>A . TAATTGGTAAGAA . 35.0 13.0 34.0 0.0 . 24 . . . none . . PASS Atlas-SNP PRKRIP1 79706 hgsc.bcm.edu hg19 7 102040095 102040095 + Silent SNP G G A novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . PRKRIP1 NM_024653 exon3 c.G306A p.K102K TGAGAAGGTCAGT . 366.0 147.0 224.0 0.0 . 25 . . . none . . PASS Atlas-SNP PRKRIP1 79706 hgsc.bcm.edu hg19 7 102040096 102040096 + Splice_Site SNP G G A novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . PRKRIP1 NM_024653 exon3 c.306+1G>A . GAGAAGGTCAGTG . 360.0 147.0 223.0 0.0 . 25 . . . none . . PASS Atlas-SNP ZNF777 27153 hgsc.bcm.edu hg19 7 149129443 149129443 + Silent SNP C C T novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . ZNF777 NM_015694 exon6 c.G1920A p.E640E GTCGCACTCGGGG . 515.0 202.0 366.0 1.0 . 63 . . . none . . PASS Atlas-SNP ZFHX4 79776 hgsc.bcm.edu hg19 8 77776650 77776650 + Nonsense_Mutation SNP C C A novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . ZFHX4 NM_024721 exon11 c.C10700A p.S3567X AAACCTCACTACC . 106.0 5.0 51.0 0.0 . 878 . . . none . . PASS Atlas-SNP CA9 768 hgsc.bcm.edu hg19 9 35674197 35674197 + Nonsense_Mutation SNP G G T novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . CA9 NM_001216 exon1 c.G241T p.E81X GGAGAGGAGGATC . 84.0 23.0 112.0 0.0 . 48 . . . none . . PASS Atlas-SNP ECD 11319 hgsc.bcm.edu hg19 10 74896486 74896486 + Missense_Mutation SNP T T G novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . ECD NM_001135752 exon14 c.A1779C p.K593N GAAACTTTTGCTG . 179.0 75.0 225.0 0.0 . 50 . . . none . . PASS Atlas-SNP COX15 1355 hgsc.bcm.edu hg19 10 101491791 101491791 + Missense_Mutation SNP A A C novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . COX15 NM_078470 exon1 c.T16G p.F6V GCGGAAAGAGCAA . 56.0 18.0 56.0 0.0 . 25 . . . none . . PASS Atlas-SNP E2F8 79733 hgsc.bcm.edu hg19 11 19251275 19251275 + Missense_Mutation SNP A A T novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . E2F8 NM_001256372 exon10 c.T1619A p.L540Q GGGCTCAGGCCTT . 410.0 146.0 448.0 0.0 . 84 . . . none . . PASS Atlas-SNP QSER1 79832 hgsc.bcm.edu hg19 11 32954930 32954930 + Nonsense_Mutation SNP C C A novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . QSER1 NM_001076786 exon4 c.C1739A p.S580X TTGAGTCATCAAC . 48.0 14.0 47.0 0.0 . 153 . . . none . . PASS Atlas-SNP MADD 8567 hgsc.bcm.edu hg19 11 47304129 47304129 + Missense_Mutation SNP T T G novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . MADD NM_130474 exon9 c.T1667G p.L556R GGATCCTTAACCC . 137.0 50.0 138.0 0.0 . 172 . . . none . . PASS Atlas-SNP HSPA8 3312 hgsc.bcm.edu hg19 11 122931912 122931912 + Missense_Mutation SNP A A G rs75739900 bycluster TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . HSPA8 NM_006597 exon2 c.T121C p.Y41H CGACATAGCTTGG . 150.0 6.0 204.0 0.0 . 168 . . . weak . . PASS Atlas-SNP PIK3C2G 5288 hgsc.bcm.edu hg19 12 18658292 18658292 + Missense_Mutation SNP G G A novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . PIK3C2G NM_004570 exon23 c.G3097A p.D1033N GTATGTGACCGTC . 11.0 7.0 16.0 0.0 . 315 . . . none . . PASS Atlas-SNP PDZRN4 29951 hgsc.bcm.edu hg19 12 41585335 41585335 + Nonsense_Mutation SNP C C T novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . PDZRN4 NM_001164595 exon2 c.C724T p.R242X GGAGGTCGACCAA . 105.0 34.0 56.0 0.0 . 346 . . . none . . PASS Atlas-SNP ACAD10 80724 hgsc.bcm.edu hg19 12 112184083 112184083 + Missense_Mutation SNP C C A novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . ACAD10 NM_001136538 exon15 c.C2344A p.P782T TATGCCCCCGAGG . 339.0 89.0 265.0 0.0 . 93 . . . none . . PASS Atlas-SNP TMEM132D 121256 hgsc.bcm.edu hg19 12 130184819 130184819 + Silent SNP C C G novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . TMEM132D NM_133448 exon2 c.G504C p.L168L GACCCTCAGGCAC . 103.0 57.0 96.0 0.0 . 299 . . . none . . PASS Atlas-SNP SLC46A3 283537 hgsc.bcm.edu hg19 13 29287510 29287510 + Missense_Mutation SNP A A G novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . SLC46A3 NM_181785 exon3 c.T367C p.Y123H CAAAATAGCAAAG . 54.0 13.0 68.0 0.0 . 86 . . . none . . PASS Atlas-SNP ATP7B 540 hgsc.bcm.edu hg19 13 52548108 52548108 + Silent SNP A A T novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . ATP7B NM_000053 exon2 c.T1248A p.A416A TTCTATAGCAGCT . 245.0 90.0 201.0 0.0 . 123 . . . none . . PASS Atlas-SNP RNF219 79596 hgsc.bcm.edu hg19 13 79190506 79190506 + Missense_Mutation SNP T T A novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . RNF219 NM_024546 exon6 c.A1390T p.T464S ATCCTGTCTTTGG . 58.0 25.0 34.0 0.0 . 94 . . . none . . PASS Atlas-SNP SDR39U1 56948 hgsc.bcm.edu hg19 14 24910963 24910963 + Missense_Mutation SNP C C G novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 SDR39U1,colon,carcinoma,0,1 SDR39U1 NM_020195 exon4 c.G245C p.R82P TCTAGGCGGCTGC . 74.0 6.0 84.0 0.0 . 19 . . . none . . PASS Atlas-SNP SPINT1 6692 hgsc.bcm.edu hg19 15 41146021 41146021 + Silent SNP C C T novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . SPINT1 NM_181642 exon5 c.C855T p.G285G CTTGGGCAACAAG . 317.0 106.0 391.0 0.0 . 28 . . . none . . PASS Atlas-SNP TP53BP1 7158 hgsc.bcm.edu hg19 15 43724401 43724401 + Silent SNP G G A novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . TP53BP1 NM_001141980 exon17 c.C3666T p.L1222L GCTATGGAGCGAC . 37.0 13.0 48.0 0.0 . 157 . . . none . . PASS Atlas-SNP CGNL1 84952 hgsc.bcm.edu hg19 15 57730838 57730838 + Missense_Mutation SNP C C G novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . CGNL1 NM_001252335 exon3 c.C641G p.T214R GTGTGACAGCTAT . 467.0 169.0 625.0 1.0 . 125 . . . none . . PASS Atlas-SNP MCTP2 55784 hgsc.bcm.edu hg19 15 94841734 94841734 + Silent SNP C C T novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . MCTP2 NM_001159643 exon1 c.C240T p.S80S GCCCAGCAGTCTG . 261.0 80.0 359.0 0.0 . 122 . . . none . . PASS Atlas-SNP ATAD5 79915 hgsc.bcm.edu hg19 17 29220728 29220728 + Missense_Mutation SNP T T G novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . ATAD5 NM_024857 exon21 c.T4857G p.N1619K AAACAATCCAGAG . 126.0 28.0 120.0 0.0 . 150 . . . none . . PASS Atlas-SNP TANC2 26115 hgsc.bcm.edu hg19 17 61466867 61466867 + Missense_Mutation SNP C C A novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . TANC2 NM_025185 exon15 c.C2791A p.L931M GGGTACCTGAGCA . 57.0 28.0 29.0 0.0 . 266 . . . none . . PASS Atlas-SNP SALL3 27164 hgsc.bcm.edu hg19 18 76754972 76754972 + Missense_Mutation SNP T T C novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . SALL3 NM_171999 exon2 c.T2981C p.I994T TGGAAATCCACTA . 86.0 33.0 148.0 0.0 . 162 . . . none . . PASS Atlas-SNP DOT1L 84444 hgsc.bcm.edu hg19 19 2191111 2191111 + Missense_Mutation SNP C C G novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . DOT1L NM_032482 exon5 c.C365G p.P122R CCGACCCCGAGAA . 116.0 41.0 122.0 0.0 . 205 . . . none . . PASS Atlas-SNP CASP14 23581 hgsc.bcm.edu hg19 19 15164633 15164633 + Silent SNP C C T novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . CASP14 NM_012114 exon4 c.C267T p.H89H GGCTCACGGGAGG . 244.0 35.0 281.0 0.0 . 44 . . . none . . PASS Atlas-SNP NWD1 284434 hgsc.bcm.edu hg19 19 16918705 16918705 + Missense_Mutation SNP G G A novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . NWD1 NM_001007525 exon18 c.G4045A p.E1349K CTGCCCGAGACCC . 404.0 153.0 475.0 0.0 . 303 . . . none . . PASS Atlas-SNP ZNF285 26974 hgsc.bcm.edu hg19 19 44896570 44896570 + Missense_Mutation SNP C C G rs144077949 bycluster;byfrequency;alternate_allele TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . ZNF285 NM_152354 exon3 c.G76C p.D26H CTTTATCCAATAG . 74.0 33.0 67.0 0.0 . 86 . . . alt C|0.997;T|0.003 . PASS Atlas-SNP ZNF665 79788 hgsc.bcm.edu hg19 19 53669370 53669370 + Missense_Mutation SNP C C G novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . ZNF665 NM_024733 exon4 c.G373C p.A125P GTTGAGCTCTTCT . 196.0 64.0 271.0 0.0 . 136 . . . none . . PASS Atlas-SNP HELZ2 85441 hgsc.bcm.edu hg19 20 62193087 62193087 + Missense_Mutation SNP T T C novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . . NM_001037335 exon13 c.A6703G p.R2235G TCCTTCTCAGGAG . 63.0 23.0 88.0 0.0 . . . . . none . . PASS Atlas-SNP LSS 4047 hgsc.bcm.edu hg19 21 47626684 47626684 + Splice_Site SNP T T G novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . LSS NM_001001438 exon17 c.1468-2A>C . AGCAGCTGAAATC . 154.0 59.0 175.0 0.0 . 50 . . . none . . PASS Atlas-SNP LONRF3 79836 hgsc.bcm.edu hg19 X 118109101 118109101 + Missense_Mutation SNP G G T novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . LONRF3 NM_001031855 exon1 c.G358T p.A120S GGCGAGGCGCTGG . 8.0 7.0 7.0 0.0 . 138 . . . none . . PASS Atlas-SNP A2ML1 144568 hgsc.bcm.edu hg19 12 9006738 9006738 + Frame_Shift_Del DEL A A - novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . A2ML1 NM_144670 exon21 c.2604delT p.F868fs . . 134.0 72.0 75.0 0.0 . 199 . 0.537313 0 none . . PASS Atlas-INDEL PTPRM 5797 hgsc.bcm.edu hg19 18 7567846 7567846 + Frame_Shift_Del DEL T T - novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . PTPRM NM_001105244 exon1 c.29delC p.T10fs . . 129.0 46.0 172.0 0.0 . 185 . 0.356589 0 none . . PASS Atlas-INDEL TOP3B 8940 hgsc.bcm.edu hg19 22 22319734 22319735 + In_Frame_Ins INS - - TTG novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . TOP3B NM_003935 exon9 c.866_867insCAA p.S289delinsTS . . 55.0 14.0 68.0 0.0 . 107 . 0.254545 0 none . . PASS Atlas-INDEL XRCC5 7520 hgsc.bcm.edu hg19 2 216981563 216981564 + Frame_Shift_Ins INS - - C novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . XRCC5 NM_021141 exon3 c.317_318insC p.D106fs . . 75.0 24.0 96.0 0.0 . 64 . 0.32 0 none . . PASS Atlas-INDEL PCDHGA4 56111 hgsc.bcm.edu hg19 5 140735217 140735218 + Frame_Shift_Ins INS - - G novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . PCDHGA4 NM_032053 exon1 c.450_451insG p.A150fs . . 77.0 22.0 110.0 0.0 . 150 . 0.285714 0 none . . PASS Atlas-INDEL GTF3C2 2976 hgsc.bcm.edu hg19 2 27565919 27565920 + Frame_Shift_Ins INS - - TGGCCTTT novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 GTF3C2,NS,malignant_melanoma,0,1 GTF3C2 NM_001035521 exon3 c.343_344insAAAGGCCA p.P115fs . . 225.0 28.0 332.0 0.0 . 73 . 0.124444 0 none . . PASS Atlas-INDEL COL5A1 1289 hgsc.bcm.edu hg19 9 137593045 137593045 + Frame_Shift_Del DEL A A - novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . COL5A1 NM_000093 exon4 c.519delC p.H173fs . . 78.0 28.0 89.0 0.0 . 323 . 0.358974 0 none . . PASS Atlas-INDEL HECA 51696 hgsc.bcm.edu hg19 6 139495590 139495590 + Frame_Shift_Del DEL A A - novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . HECA NM_016217 exon3 c.1380delC p.I460fs . . 180.0 59.0 156.0 0.0 . 45 . 0.327778 0 none . . PASS Atlas-INDEL CYP2D6 1565 hgsc.bcm.edu hg19 22 42523507 42523516 + Frame_Shift_Del DEL AGGGGGACGA AGGGGGACGA - novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 AGGGGGACGA AGGGGGACGA . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . CYP2D6 NM_000106 exon7 c.1107_1116del p.369_372del . . 147.0 14.0 205.0 0.0 . 104 . 0.0952381 0 none . . PASS Atlas-INDEL GTF3C2 2976 hgsc.bcm.edu hg19 2 27565929 27565930 + Frame_Shift_Del DEL GG GG - novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 GG GG . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 GTF3C2,NS,carcinoma,0,1 GTF3C2 NM_001035521 exon3 c.333_334del p.111_112del . . 232.0 15.0 316.0 0.0 . 73 . 0.0646552 0 none . . PASS Atlas-INDEL ZMYM6 9204 hgsc.bcm.edu hg19 1 35457962 35457962 + Frame_Shift_Del DEL T T - novel TCGA-B9-4113-01A-01D-1252-08 TCGA-B9-4113-11A-01D-1252-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 527ea66a-fb9e-4308-b49d-48226ac05304 881301ff-ec26-46fd-834f-93d9b3ec8da0 . ZMYM6 NM_007167 exon15 c.2020delT p.F674fs . . 165.0 54.0 196.0 0.0 . 110 . 0.327273 0 none . . PASS Atlas-INDEL