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 dataset type classification start end gene chr ref_allele tum_allele1 tum_allele2 context MTOR 2475 broad.mit.edu 36 1 11241933 11241933 + Missense_Mutation SNP C C A novel Unknown TCGA-25-1329-01 TCGA-25-1329-10 C A C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 11241933 11241933 MTOR 1 C C A 27 ZRANB2 9406 broad.mit.edu 36 1 71305075 71305075 + Nonsense_Mutation SNP T T A novel Unknown TCGA-25-1329-01 TCGA-25-1329-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 71305075 71305075 ZRANB2 1 T T A 56 WDR63 126820 broad.mit.edu 36 1 85311356 85311356 + Missense_Mutation SNP G G C novel Unknown TCGA-25-1329-01 TCGA-25-1329-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 85311356 85311356 WDR63 1 G G C 33 PHGDH 26227 broad.mit.edu 36 1 120086007 120086007 + Silent SNP G G A novel Unknown TCGA-25-1329-01 TCGA-25-1329-10 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 120086007 120086007 PHGDH 1 G G A 45 ITGB1 3688 broad.mit.edu 36 10 33249239 33249239 + Silent SNP G G A novel Unknown TCGA-25-1329-01 TCGA-25-1329-10 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 33249239 33249239 ITGB1 10 G G A 40 PHRF1 57661 broad.mit.edu 36 11 596502 596502 + Silent SNP G G T novel Unknown TCGA-25-1329-01 TCGA-25-1329-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 596502 596502 PHRF1 11 G G T 46 MRGPRE 116534 broad.mit.edu 36 11 3206566 3206566 + Missense_Mutation SNP C C T novel Unknown TCGA-25-1329-01 TCGA-25-1329-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 3206566 3206566 MRGPRE 11 C C T 27 OR5F1 338674 broad.mit.edu 36 11 55518619 55518619 + Missense_Mutation SNP G G A novel Unknown TCGA-25-1329-01 TCGA-25-1329-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 55518619 55518619 OR5F1 11 G G A 40 STIP1 10963 broad.mit.edu 36 11 63728108 63728108 + Missense_Mutation SNP A A T novel Unknown TCGA-25-1329-01 TCGA-25-1329-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 63728108 63728108 STIP1 11 A A T 13 C11orf65 160140 broad.mit.edu 36 11 107783049 107783049 + Missense_Mutation SNP C C T novel Unknown TCGA-25-1329-01 TCGA-25-1329-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 107783049 107783049 C11orf65 11 C C T 31 GRIK4 2900 broad.mit.edu 36 11 120281358 120281358 + Silent SNP C C T novel Unknown TCGA-25-1329-01 TCGA-25-1329-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 120281358 120281358 GRIK4 11 C C T 27 NINJ2 4815 broad.mit.edu 36 12 544825 544825 + Missense_Mutation SNP C C T novel Unknown TCGA-25-1329-01 TCGA-25-1329-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 544825 544825 NINJ2 12 C C T 23 CD163L1 283316 broad.mit.edu 36 12 7422901 7422901 + Nonsense_Mutation SNP G G A novel Unknown TCGA-25-1329-01 TCGA-25-1329-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 7422901 7422901 CD163L1 12 G G A 40 LEMD3 23592 broad.mit.edu 36 12 63849783 63849783 + Missense_Mutation SNP G G A novel Unknown TCGA-25-1329-01 TCGA-25-1329-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 63849783 63849783 LEMD3 12 G G A 37 GLIPR1L2 144321 broad.mit.edu 36 12 74102998 74102998 + Missense_Mutation SNP G G A novel Unknown TCGA-25-1329-01 TCGA-25-1329-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 74102998 74102998 GLIPR1L2 12 G G A 37 TMEM132D 121256 broad.mit.edu 36 12 128125002 128125002 + Nonsense_Mutation SNP G G A novel Unknown TCGA-25-1329-01 TCGA-25-1329-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 128125002 128125002 TMEM132D 12 G G A 47 C13orf23 80209 broad.mit.edu 36 13 38485390 38485390 + Missense_Mutation SNP T T C novel Unknown TCGA-25-1329-01 TCGA-25-1329-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 38485390 38485390 C13orf23 13 T T C 54 ANGEL1 23357 broad.mit.edu 36 14 76345445 76345445 + Missense_Mutation SNP G G A novel Unknown TCGA-25-1329-01 TCGA-25-1329-10 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 76345445 76345445 ANGEL1 14 G G A 46 DIO3 1735 broad.mit.edu 36 14 101098050 101098050 + Missense_Mutation SNP C C T novel Unknown TCGA-25-1329-01 TCGA-25-1329-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 101098050 101098050 DIO3 14 C C T 27 SRL 6345 broad.mit.edu 36 16 4194548 4194548 + Silent SNP G G A novel Unknown TCGA-25-1329-01 TCGA-25-1329-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 4194548 4194548 SRL 16 G G A 39 MIB1 57534 broad.mit.edu 36 18 17649662 17649662 + Missense_Mutation SNP T T G novel Unknown TCGA-25-1329-01 TCGA-25-1329-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 17649662 17649662 MIB1 18 T T G 64 KCNS3 3790 broad.mit.edu 36 2 17976259 17976259 + Missense_Mutation SNP G G A novel Unknown TCGA-25-1329-01 TCGA-25-1329-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 17976259 17976259 KCNS3 2 G G A 39 TTN 7273 broad.mit.edu 36 2 179349789 179349789 + Nonsense_Mutation SNP G G A novel Unknown TCGA-25-1329-01 TCGA-25-1329-10 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Nonsense_Mutation SNP 179349789 179349789 TTN 2 G G A 38 SULF2 55959 broad.mit.edu 36 20 45734476 45734476 + Silent SNP C C T novel Unknown TCGA-25-1329-01 TCGA-25-1329-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 45734476 45734476 SULF2 20 C C T 21 ATP9A 10079 broad.mit.edu 36 20 49657506 49657506 + Missense_Mutation SNP A A C novel Unknown TCGA-25-1329-01 TCGA-25-1329-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 49657506 49657506 ATP9A 20 A A C 4 EPHB1 2047 broad.mit.edu 36 3 136334264 136334264 + Missense_Mutation SNP G G A novel Unknown TCGA-25-1329-01 TCGA-25-1329-10 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 136334264 136334264 EPHB1 3 G G A 38 MFAP3L 9848 broad.mit.edu 36 4 171149977 171149977 + Missense_Mutation SNP G G T novel Unknown TCGA-25-1329-01 TCGA-25-1329-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 171149977 171149977 MFAP3L 4 G G T 44 SLC6A18 348932 broad.mit.edu 36 5 1285360 1285360 + Missense_Mutation SNP G G A novel Unknown TCGA-25-1329-01 TCGA-25-1329-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 1285360 1285360 SLC6A18 5 G G A 38 PRDM9 56979 broad.mit.edu 36 5 23562102 23562102 + Missense_Mutation SNP C C G novel Unknown TCGA-25-1329-01 TCGA-25-1329-10 C G C C Unknown Valid Somatic x x 454_PCR_WGA x Broad Missense_Mutation SNP 23562102 23562102 PRDM9 5 C C G 21 ZFP57 346171 broad.mit.edu 36 6 29748583 29748583 + Silent SNP G G A novel Unknown TCGA-25-1329-01 TCGA-25-1329-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 29748583 29748583 ZFP57 6 G G A 45 C6orf27 80737 broad.mit.edu 36 6 31842069 31842069 + Silent SNP C C T novel Unknown TCGA-25-1329-01 TCGA-25-1329-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 31842069 31842069 C6orf27 6 C C T 23 CENPQ 55166 broad.mit.edu 36 6 49556675 49556675 + Missense_Mutation SNP T T G novel Unknown TCGA-25-1329-01 TCGA-25-1329-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 49556675 49556675 CENPQ 6 T T G 64 CHN2 1124 broad.mit.edu 36 7 29513396 29513396 + Missense_Mutation SNP A A T novel Unknown TCGA-25-1329-01 TCGA-25-1329-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 29513396 29513396 CHN2 7 A A T 4 RSBN1L 222194 broad.mit.edu 36 7 77163736 77163736 + Missense_Mutation SNP C C T novel Unknown TCGA-25-1329-01 TCGA-25-1329-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 77163736 77163736 RSBN1L 7 C C T 23 TNFRSF10A 8797 broad.mit.edu 36 8 23116183 23116183 + Missense_Mutation SNP C C T novel Unknown TCGA-25-1329-01 TCGA-25-1329-10 C T C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 23116183 23116183 TNFRSF10A 8 C C T 23 MCART1 92014 broad.mit.edu 36 9 37878379 37878379 + Nonsense_Mutation SNP G G A novel Unknown TCGA-25-1329-01 TCGA-25-1329-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 37878379 37878379 MCART1 9 G G A 37 PRPF4 9128 broad.mit.edu 36 9 115093655 115093655 + Missense_Mutation SNP T T A novel Unknown TCGA-25-1329-01 TCGA-25-1329-10 T A T T Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 115093655 115093655 PRPF4 9 T T A 55 COL5A1 1289 broad.mit.edu 36 9 136856317 136856317 + Silent SNP G G A novel Unknown TCGA-25-1329-01 TCGA-25-1329-10 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 136856317 136856317 COL5A1 9 G G A 38 TP53 7157 broad.mit.edu 36 17 7520272 7520272 + Frame_Shift_Del DEL G G - novel Unknown TCGA-25-1329-01 TCGA-25-1329-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Del DEL 7520272 7520272 TP53 17 G G - 39 CEACAM18 729767 broad.mit.edu 36 19 56675630 56675631 + Frame_Shift_Del DEL AC - AC novel Unknown TCGA-25-1329-01 TCGA-25-1329-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Del DEL 56675630 56675631 CEACAM18 19 AC - AC 2