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 11174395 11174395 + Missense_Mutation SNP A A T novel TCGA-MH-A857-01A-11D-A34Z-10 TCGA-MH-A857-10A-01D-A34Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0299221a-3d27-41da-acfa-e3d9a0bf59cf 66cc7636-90d2-4545-99c6-ea90745ba8b1 MTOR,NS,carcinoma,+1,2 MTOR NM_004958 exon53 c.T7280A p.L2427Q CAGTTCAGCAAGG . 44.0 14.0 70.0 0.0 . 327 . . . none . . PASS Atlas-SNP DENND2C 163259 hgsc.bcm.edu hg19 1 115130431 115130431 + Silent SNP G G T novel TCGA-MH-A857-01A-11D-A34Z-10 TCGA-MH-A857-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0299221a-3d27-41da-acfa-e3d9a0bf59cf 66cc7636-90d2-4545-99c6-ea90745ba8b1 . DENND2C NM_001256404 exon19 c.C2574A p.S858S ACTTCGGGAGGTG . 95.0 5.0 149.0 0.0 . 105 . . . none . . PASS Atlas-SNP LYST 1130 hgsc.bcm.edu hg19 1 235827769 235827769 + Missense_Mutation SNP C C A novel TCGA-MH-A857-01A-11D-A34Z-10 TCGA-MH-A857-10A-01D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0299221a-3d27-41da-acfa-e3d9a0bf59cf 66cc7636-90d2-4545-99c6-ea90745ba8b1 . LYST NM_000081 exon51 c.G11191T p.V3731L ACCTTACAATTCC . 60.0 20.0 81.0 0.0 . 370 . . . none . . PASS Atlas-SNP B3GNT2 10678 hgsc.bcm.edu hg19 2 62449390 62449390 + Missense_Mutation SNP G G A novel TCGA-MH-A857-01A-11D-A34Z-10 TCGA-MH-A857-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0299221a-3d27-41da-acfa-e3d9a0bf59cf 66cc7636-90d2-4545-99c6-ea90745ba8b1 . B3GNT2 NM_006577 exon2 c.G35A p.G12D TGTTGGGTATCCT . 99.0 31.0 179.0 0.0 . 34 . . . none . . PASS Atlas-SNP ST3GAL6 10402 hgsc.bcm.edu hg19 3 98512536 98512536 + Silent SNP G G T novel TCGA-MH-A857-01A-11D-A34Z-10 TCGA-MH-A857-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0299221a-3d27-41da-acfa-e3d9a0bf59cf 66cc7636-90d2-4545-99c6-ea90745ba8b1 . ST3GAL6 NM_001271145 exon10 c.G1086T p.V362V CAATGTGACTGCA . 87.0 25.0 140.0 0.0 . 41 . . . none . . PASS Atlas-SNP DSPP 1834 hgsc.bcm.edu hg19 4 88537513 88537513 + Missense_Mutation SNP A A C rs112275895 TCGA-MH-A857-01A-11D-A34Z-10 TCGA-MH-A857-10A-01D-A34Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0299221a-3d27-41da-acfa-e3d9a0bf59cf 66cc7636-90d2-4545-99c6-ea90745ba8b1 . DSPP NM_014208 exon5 c.A3699C p.E1233D CAATGAAAGCAGC . 88.0 13.0 116.0 0.0 . 174 . . . weak A|0.500;C|0.500 0.500 PASS Atlas-SNP PCDHA10 56139 hgsc.bcm.edu hg19 5 140236456 140236456 + Nonsense_Mutation SNP G G T novel TCGA-MH-A857-01A-11D-A34Z-10 TCGA-MH-A857-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0299221a-3d27-41da-acfa-e3d9a0bf59cf 66cc7636-90d2-4545-99c6-ea90745ba8b1 . PCDHA10 NM_031859 exon1 c.G823T p.E275X AACAAGGAAATGA . 127.0 52.0 158.0 0.0 . 358 . . . none . . PASS Atlas-SNP ERGIC1 57222 hgsc.bcm.edu hg19 5 172362237 172362237 + Missense_Mutation SNP G G T novel TCGA-MH-A857-01A-11D-A34Z-10 TCGA-MH-A857-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0299221a-3d27-41da-acfa-e3d9a0bf59cf 66cc7636-90d2-4545-99c6-ea90745ba8b1 . ERGIC1 NM_001031711 exon9 c.G689T p.W230L CAATCTGGTTCCG . 83.0 4.0 113.0 0.0 . 35 . . . none . . PASS Atlas-SNP ATAT1 79969 hgsc.bcm.edu hg19 6 30594987 30594987 + Silent SNP T T C novel TCGA-MH-A857-01A-11D-A34Z-10 TCGA-MH-A857-10A-01D-A34Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0299221a-3d27-41da-acfa-e3d9a0bf59cf 66cc7636-90d2-4545-99c6-ea90745ba8b1 ATAT1_ENST00000330083,NS,carcinoma,0,1 ATAT1 NM_001031722 exon1 c.T7C p.L3L ATGTGGTTGACCT . 70.0 28.0 103.0 1.0 . 30 . . . none . . PASS Atlas-SNP CDSN 1041 hgsc.bcm.edu hg19 6 31085252 31085252 + Missense_Mutation SNP C C T rs370680006 TCGA-MH-A857-01A-11D-A34Z-10 TCGA-MH-A857-10A-01D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0299221a-3d27-41da-acfa-e3d9a0bf59cf 66cc7636-90d2-4545-99c6-ea90745ba8b1 . CDSN NM_001264 exon2 c.G140A p.R47H GTGATACGCGTGG . 57.0 12.0 102.0 0.0 . 48 . . . weak . . PASS Atlas-SNP NPC1L1 29881 hgsc.bcm.edu hg19 7 44561797 44561797 + Silent SNP G G A novel TCGA-MH-A857-01A-11D-A34Z-10 TCGA-MH-A857-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0299221a-3d27-41da-acfa-e3d9a0bf59cf 66cc7636-90d2-4545-99c6-ea90745ba8b1 . NPC1L1 NM_001101648 exon11 c.C2682T p.F894F CACCTCGAAGTAG . 21.0 7.0 40.0 0.0 . 141 . . . none . . PASS Atlas-SNP SEMA3E 9723 hgsc.bcm.edu hg19 7 83037688 83037688 + Silent SNP C C T novel TCGA-MH-A857-01A-11D-A34Z-10 TCGA-MH-A857-10A-01D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0299221a-3d27-41da-acfa-e3d9a0bf59cf 66cc7636-90d2-4545-99c6-ea90745ba8b1 . SEMA3E NM_012431 exon6 c.G666A p.L222L ACCTTTCAACAGA . 108.0 27.0 171.0 0.0 . 125 . . . none . . PASS Atlas-SNP MLLT3 4300 hgsc.bcm.edu hg19 9 20414373 20414373 + Silent SNP G G A novel TCGA-MH-A857-01A-11D-A34Z-10 TCGA-MH-A857-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0299221a-3d27-41da-acfa-e3d9a0bf59cf 66cc7636-90d2-4545-99c6-ea90745ba8b1 MLLT3,NS,carcinoma,0,4 MLLT3 NM_004529 exon5 c.C471T p.S157S GCTGCTGCTACTG . 96.0 6.0 110.0 1.0 . 125 . . . none . . PASS Atlas-SNP SVIL 6840 hgsc.bcm.edu hg19 10 29818641 29818641 + Missense_Mutation SNP C C T novel TCGA-MH-A857-01A-11D-A34Z-10 TCGA-MH-A857-10A-01D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0299221a-3d27-41da-acfa-e3d9a0bf59cf 66cc7636-90d2-4545-99c6-ea90745ba8b1 . SVIL NM_021738 exon12 c.G2239A p.A747T TGGCTGCGATGAC . 60.0 4.0 98.0 0.0 . 226 . . . none . . PASS Atlas-SNP PIWIL4 143689 hgsc.bcm.edu hg19 11 94300728 94300728 + Missense_Mutation SNP G G A novel TCGA-MH-A857-01A-11D-A34Z-10 TCGA-MH-A857-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0299221a-3d27-41da-acfa-e3d9a0bf59cf 66cc7636-90d2-4545-99c6-ea90745ba8b1 . PIWIL4 NM_152431 exon1 c.G44A p.S15N CCCGCAGCCCCAG . 71.0 25.0 105.0 0.0 . 70 . . . none . . PASS Atlas-SNP C2CD5 9847 hgsc.bcm.edu hg19 12 22676361 22676361 + Missense_Mutation SNP C C T novel TCGA-MH-A857-01A-11D-A34Z-10 TCGA-MH-A857-10A-01D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0299221a-3d27-41da-acfa-e3d9a0bf59cf 66cc7636-90d2-4545-99c6-ea90745ba8b1 . . NM_014802 exon7 c.G799A p.E267K CTTACTCCTTCAT . 104.0 29.0 133.0 0.0 . . . . . none . . PASS Atlas-SNP PTPRR 5801 hgsc.bcm.edu hg19 12 71286725 71286725 + Missense_Mutation SNP C C T novel TCGA-MH-A857-01A-11D-A34Z-10 TCGA-MH-A857-10A-01D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0299221a-3d27-41da-acfa-e3d9a0bf59cf 66cc7636-90d2-4545-99c6-ea90745ba8b1 . PTPRR NM_002849 exon2 c.G91A p.A31T TAATTGCCAAAAA . 243.0 79.0 276.0 0.0 . 109 . . . none . . PASS Atlas-SNP RNF17 56163 hgsc.bcm.edu hg19 13 25428149 25428149 + Missense_Mutation SNP T T G novel TCGA-MH-A857-01A-11D-A34Z-10 TCGA-MH-A857-10A-01D-A34Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0299221a-3d27-41da-acfa-e3d9a0bf59cf 66cc7636-90d2-4545-99c6-ea90745ba8b1 . RNF17 NM_031277 exon25 c.T3477G p.F1159L TGAATTTCAGGAG . 98.0 27.0 121.0 0.0 . 259 . . . none . . PASS Atlas-SNP EML5 161436 hgsc.bcm.edu hg19 14 89109293 89109293 + Missense_Mutation SNP C C T novel TCGA-MH-A857-01A-11D-A34Z-10 TCGA-MH-A857-10A-01D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0299221a-3d27-41da-acfa-e3d9a0bf59cf 66cc7636-90d2-4545-99c6-ea90745ba8b1 . EML5 NM_183387 exon30 c.G4181A p.G1394D TCATCACCATCAT . 143.0 11.0 229.0 0.0 . 141 . . . none . . PASS Atlas-SNP CGNL1 84952 hgsc.bcm.edu hg19 15 57815687 57815687 + Missense_Mutation SNP G G A novel TCGA-MH-A857-01A-11D-A34Z-10 TCGA-MH-A857-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0299221a-3d27-41da-acfa-e3d9a0bf59cf 66cc7636-90d2-4545-99c6-ea90745ba8b1 . CGNL1 NM_001252335 exon12 c.G2716A p.G906R TTGCAGGGAAATC . 53.0 17.0 87.0 0.0 . 125 . . . none . . PASS Atlas-SNP EPG5 57724 hgsc.bcm.edu hg19 18 43534423 43534423 + Silent SNP T T C novel TCGA-MH-A857-01A-11D-A34Z-10 TCGA-MH-A857-10A-01D-A34Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0299221a-3d27-41da-acfa-e3d9a0bf59cf 66cc7636-90d2-4545-99c6-ea90745ba8b1 . EPG5 NM_020964 exon2 c.A945G p.T315T ATCAGATGTCAGA . 113.0 38.0 174.0 0.0 . 199 . . . none . . PASS Atlas-SNP MAG 4099 hgsc.bcm.edu hg19 19 35802844 35802844 + Missense_Mutation SNP G G A novel TCGA-MH-A857-01A-11D-A34Z-10 TCGA-MH-A857-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0299221a-3d27-41da-acfa-e3d9a0bf59cf 66cc7636-90d2-4545-99c6-ea90745ba8b1 . MAG NM_080600 exon10 c.G1640A p.S547N GCCCCAGCTTCTC . 83.0 37.0 140.0 0.0 . 172 . . . none . . PASS Atlas-SNP SCAF1 58506 hgsc.bcm.edu hg19 19 50156129 50156129 + Missense_Mutation SNP C C A novel TCGA-MH-A857-01A-11D-A34Z-10 TCGA-MH-A857-10A-01D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0299221a-3d27-41da-acfa-e3d9a0bf59cf 66cc7636-90d2-4545-99c6-ea90745ba8b1 . SCAF1 NM_021228 exon7 c.C2483A p.S828Y GTTCTTCCCGGAA . 26.0 9.0 57.0 0.0 . 78 . . . none . . PASS Atlas-SNP COX1 5742 hgsc.bcm.edu hg19 MT 6054 6054 + Missense_Mutation SNP G G A novel TCGA-MH-A857-01A-11D-A34Z-10 TCGA-MH-A857-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0299221a-3d27-41da-acfa-e3d9a0bf59cf 66cc7636-90d2-4545-99c6-ea90745ba8b1 . . ENST00000361624 exon1 c.G151A p.D51N GGTAACGACCACA . 118.0 8.0 11.0 0.0 . . . . . none . . PASS Atlas-SNP COX2 5743 hgsc.bcm.edu hg19 MT 8075 8075 + Missense_Mutation SNP G G A novel TCGA-MH-A857-01A-11D-A34Z-10 TCGA-MH-A857-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0299221a-3d27-41da-acfa-e3d9a0bf59cf 66cc7636-90d2-4545-99c6-ea90745ba8b1 . . ENST00000361739 exon1 c.G490A p.A164T TCATGAGCTGTCC . 80.0 6.0 14.0 0.0 . . . . . none . . PASS Atlas-SNP MLL 4297 hgsc.bcm.edu hg19 11 118377019 118377019 + Frame_Shift_Del DEL C C - novel TCGA-MH-A857-01A-11D-A34Z-10 TCGA-MH-A857-10A-01D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0299221a-3d27-41da-acfa-e3d9a0bf59cf 66cc7636-90d2-4545-99c6-ea90745ba8b1 . MLL NM_001197104 exon27 c.10411delT p.S3471fs . . 90.0 34.0 112.0 0.0 . 548 . 0.377778 0 none . . PASS Atlas-Indel,Pindel EFHB 151651 hgsc.bcm.edu hg19 3 19947241 19947250 + Frame_Shift_Del DEL CCTGTGGAAA CCTGTGGAAA - novel TCGA-MH-A857-01A-11D-A34Z-10 TCGA-MH-A857-10A-01D-A34Z-10 CCTGTGGAAA CCTGTGGAAA . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0299221a-3d27-41da-acfa-e3d9a0bf59cf 66cc7636-90d2-4545-99c6-ea90745ba8b1 . EFHB NM_144715 exon6 c.1289_1290del p.430_430del . . 65.0 15.0 124.0 0.0 . 186 . 0.230769 0 none . . PASS Atlas-Indel,Pindel NCOA6 23054 hgsc.bcm.edu hg19 20 33329080 33329081 + Frame_Shift_Del DEL AA AA - novel TCGA-MH-A857-01A-11D-A34Z-10 TCGA-MH-A857-10A-01D-A34Z-10 AA AA . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0299221a-3d27-41da-acfa-e3d9a0bf59cf 66cc7636-90d2-4545-99c6-ea90745ba8b1 . NCOA6 NM_014071 exon11 c.4980_4981del p.1660_1661del . . 68.0 23.0 109.0 0.0 . 219 . 0.338235 0 none . . PASS Atlas-Indel,Pindel OBSCN 84033 hgsc.bcm.edu hg19 1 228547456 228547466 + Frame_Shift_Del DEL GCAGGCCGGAG GCAGGCCGGAG - novel TCGA-MH-A857-01A-11D-A34Z-10 TCGA-MH-A857-10A-01D-A34Z-10 GCAGGCCGGAG GCAGGCCGGAG . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 0299221a-3d27-41da-acfa-e3d9a0bf59cf 66cc7636-90d2-4545-99c6-ea90745ba8b1 . OBSCN NM_052843 exon81 c.18862_18872del p.6288_6291del . . 54.0 13.0 104.0 0.0 . 2142 . 0.240741 0 none . . PASS Atlas-Indel,Pindel