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 UBE2J2 118424 broad.mit.edu 36 1 1182541 1182541 + Missense_Mutation SNP T T A novel Unknown TCGA-25-1320-01 TCGA-25-1320-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 1182541 1182541 UBE2J2 1 T T A 51 CROCC 9696 broad.mit.edu 36 1 17154522 17154522 + Silent SNP A A G novel Unknown TCGA-25-1320-01 TCGA-25-1320-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 17154522 17154522 CROCC 1 A A G 7 TM2D1 83941 broad.mit.edu 36 1 61947587 61947587 + Splice_Site_SNP SNP A A C novel Unknown TCGA-25-1320-01 TCGA-25-1320-10 Unknown Unknown Unknown x x --- x Broad Splice_Site_SNP SNP 61947587 61947587 TM2D1 1 A A C 14 VAV3 10451 broad.mit.edu 36 1 108112631 108112631 + Silent SNP T T C novel Unknown TCGA-25-1320-01 TCGA-25-1320-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 108112631 108112631 VAV3 1 T T C 50 GNAI3 2773 broad.mit.edu 36 1 109917913 109917913 + Silent SNP G G A novel Unknown TCGA-25-1320-01 TCGA-25-1320-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 109917913 109917913 GNAI3 1 G G A 45 SNX27 81609 broad.mit.edu 36 1 149907704 149907704 + Missense_Mutation SNP A A G novel Unknown TCGA-25-1320-01 TCGA-25-1320-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 149907704 149907704 SNX27 1 A A G 4 RHBG 57127 broad.mit.edu 36 1 154614686 154614686 + Missense_Mutation SNP C C A novel Unknown TCGA-25-1320-01 TCGA-25-1320-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 154614686 154614686 RHBG 1 C C A 30 IRF6 3664 broad.mit.edu 36 1 208035326 208035326 + Missense_Mutation SNP T T C novel Unknown TCGA-25-1320-01 TCGA-25-1320-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 208035326 208035326 IRF6 1 T T C 62 MUC2 4583 broad.mit.edu 36 11 1072622 1072622 + Missense_Mutation SNP A A G novel Unknown TCGA-25-1320-01 TCGA-25-1320-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 1072622 1072622 MUC2 11 A A G 4 ACRBP 84519 broad.mit.edu 36 12 6626372 6626372 + Silent SNP A A C novel Unknown TCGA-25-1320-01 TCGA-25-1320-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 6626372 6626372 ACRBP 12 A A C 11 A2ML1 144568 broad.mit.edu 36 12 8912192 8912192 + Nonsense_Mutation SNP C C T novel Unknown TCGA-25-1320-01 TCGA-25-1320-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 8912192 8912192 A2ML1 12 C C T 31 LRRK2 120892 broad.mit.edu 36 12 38954744 38954744 + Missense_Mutation SNP A A C novel Unknown TCGA-25-1320-01 TCGA-25-1320-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 38954744 38954744 LRRK2 12 A A C 3 ADAMTS20 80070 broad.mit.edu 36 12 42110486 42110486 + Missense_Mutation SNP T T A novel Unknown TCGA-25-1320-01 TCGA-25-1320-10 T A T T Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 42110486 42110486 ADAMTS20 12 T T A 54 TRPC4 7223 broad.mit.edu 36 13 37109441 37109441 + Missense_Mutation SNP A A T novel Unknown TCGA-25-1320-01 TCGA-25-1320-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 37109441 37109441 TRPC4 13 A A T 3 TRPC4 7223 broad.mit.edu 36 13 37123457 37123457 + Missense_Mutation SNP G G A novel Unknown TCGA-25-1320-01 TCGA-25-1320-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 37123457 37123457 TRPC4 13 G G A 48 CCDC88C 440193 broad.mit.edu 36 14 90827168 90827169 + Missense_Mutation DNP CA CA AC novel Unknown TCGA-25-1320-01 TCGA-25-1320-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation DNP 90827168 90827169 CCDC88C 14 CA CA AC 25 C15orf2 23742 broad.mit.edu 36 15 22472629 22472629 + Silent SNP C C T novel Unknown TCGA-25-1320-01 TCGA-25-1320-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 22472629 22472629 C15orf2 15 C C T 19 KIAA1199 57214 broad.mit.edu 36 15 78960497 78960497 + Silent SNP C C T novel Unknown TCGA-25-1320-01 TCGA-25-1320-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 78960497 78960497 KIAA1199 15 C C T 31 BNC1 646 broad.mit.edu 36 15 81723796 81723796 + Missense_Mutation SNP C C T novel Unknown TCGA-25-1320-01 TCGA-25-1320-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 81723796 81723796 BNC1 15 C C T 27 NMB 4828 broad.mit.edu 36 15 82999553 82999553 + Silent SNP C C T novel Unknown TCGA-25-1320-01 TCGA-25-1320-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 82999553 82999553 NMB 15 C C T 24 TSC2 7249 broad.mit.edu 36 16 2069154 2069154 + Missense_Mutation SNP G G T novel Unknown TCGA-25-1320-01 TCGA-25-1320-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 2069154 2069154 TSC2 16 G G T 45 EEF2K 29904 broad.mit.edu 36 16 22185593 22185593 + Silent SNP C C T novel Unknown TCGA-25-1320-01 TCGA-25-1320-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 22185593 22185593 EEF2K 16 C C T 30 EEF2K 29904 broad.mit.edu 36 16 22185672 22185672 + Missense_Mutation SNP C C T novel Unknown TCGA-25-1320-01 TCGA-25-1320-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 22185672 22185672 EEF2K 16 C C T 29 SMPD3 55512 broad.mit.edu 36 16 66962930 66962930 + Missense_Mutation SNP T T C novel Unknown TCGA-25-1320-01 TCGA-25-1320-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 66962930 66962930 SMPD3 16 T T C 59 FAM83G 644815 broad.mit.edu 36 17 18822350 18822350 + Missense_Mutation SNP T T A novel Unknown TCGA-25-1320-01 TCGA-25-1320-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 18822350 18822350 FAM83G 17 T T A 59 SCN4A 6329 broad.mit.edu 36 17 59378218 59378218 + Silent SNP C C T novel Unknown TCGA-25-1320-01 TCGA-25-1320-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 59378218 59378218 SCN4A 17 C C T 23 CNDP2 55748 broad.mit.edu 36 18 70334551 70334551 + Missense_Mutation SNP G G A novel Unknown TCGA-25-1320-01 TCGA-25-1320-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 70334551 70334551 CNDP2 18 G G A 47 DOT1L 84444 broad.mit.edu 36 19 2161819 2161821 + Missense_Mutation TNP AGA AGA CCG novel Unknown TCGA-25-1320-01 TCGA-25-1320-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation TNP 2161819 2161821 DOT1L 19 AGA AGA CCG 7 RDH8 50700 broad.mit.edu 36 19 9993084 9993084 + Silent SNP C C T novel Unknown TCGA-25-1320-01 TCGA-25-1320-10 C T C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 9993084 9993084 RDH8 19 C C T 23 NCAN 1463 broad.mit.edu 36 19 19200041 19200041 + Missense_Mutation SNP C C T novel Unknown TCGA-25-1320-01 TCGA-25-1320-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 19200041 19200041 NCAN 19 C C T 19 ZNF536 9745 broad.mit.edu 36 19 35628320 35628320 + Missense_Mutation SNP C C T novel Unknown TCGA-25-1320-01 TCGA-25-1320-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 35628320 35628320 ZNF536 19 C C T 27 SP100 6672 broad.mit.edu 36 2 231040173 231040173 + Silent SNP G G A novel Unknown TCGA-25-1320-01 TCGA-25-1320-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 231040173 231040173 SP100 2 G G A 35 GIGYF2 26058 broad.mit.edu 36 2 233367824 233367824 + Missense_Mutation SNP G G T novel Unknown TCGA-25-1320-01 TCGA-25-1320-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 233367824 233367824 GIGYF2 2 G G T 36 TTI1 9675 broad.mit.edu 36 20 36075196 36075196 + Missense_Mutation SNP G G C novel Unknown TCGA-25-1320-01 TCGA-25-1320-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 36075196 36075196 TTI1 20 G G C 41 MRPS25 64432 broad.mit.edu 36 3 15075893 15075893 + Silent SNP C C T novel Unknown TCGA-25-1320-01 TCGA-25-1320-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 15075893 15075893 MRPS25 3 C C T 25 NBEAL2 23218 broad.mit.edu 36 3 47014167 47014167 + Silent SNP C C A novel Unknown TCGA-25-1320-01 TCGA-25-1320-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 47014167 47014167 NBEAL2 3 C C A 29 PCYT1A 5130 broad.mit.edu 36 3 197481734 197481734 + Silent SNP G G A novel Unknown TCGA-25-1320-01 TCGA-25-1320-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 197481734 197481734 PCYT1A 3 G G A 40 PIGZ 80235 broad.mit.edu 36 3 198158883 198158883 + Missense_Mutation SNP C C T novel Unknown TCGA-25-1320-01 TCGA-25-1320-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 198158883 198158883 PIGZ 3 C C T 23 POLN 353497 broad.mit.edu 36 4 2044518 2044518 + Missense_Mutation SNP A A C novel Unknown TCGA-25-1320-01 TCGA-25-1320-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 2044518 2044518 POLN 4 A A C 6 ADAMTS16 170690 broad.mit.edu 36 5 5288235 5288235 + Silent SNP C C T novel Unknown TCGA-25-1320-01 TCGA-25-1320-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 5288235 5288235 ADAMTS16 5 C C T 23 STC2 8614 broad.mit.edu 36 5 172677475 172677475 + Missense_Mutation SNP T T A novel Unknown TCGA-25-1320-01 TCGA-25-1320-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 172677475 172677475 STC2 5 T T A 49 RUFY1 80230 broad.mit.edu 36 5 178928940 178928940 + Missense_Mutation SNP G G A novel Unknown TCGA-25-1320-01 TCGA-25-1320-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 178928940 178928940 RUFY1 5 G G A 41 PPP1R10 5514 broad.mit.edu 36 6 30680387 30680387 + Silent SNP G G A novel Unknown TCGA-25-1320-01 TCGA-25-1320-10 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 30680387 30680387 PPP1R10 6 G G A 46 RARS2 57038 broad.mit.edu 36 6 88315054 88315054 + Missense_Mutation SNP A A C novel Unknown TCGA-25-1320-01 TCGA-25-1320-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 88315054 88315054 RARS2 6 A A C 2 MICALL2 79778 broad.mit.edu 36 7 1442910 1442910 + Missense_Mutation SNP C C G novel Unknown TCGA-25-1320-01 TCGA-25-1320-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 1442910 1442910 MICALL2 7 C C G 23 FBXL18 80028 broad.mit.edu 36 7 5506814 5506814 + Missense_Mutation SNP G G A novel Unknown TCGA-25-1320-01 TCGA-25-1320-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 5506814 5506814 FBXL18 7 G G A 34 BAZ1B 9031 broad.mit.edu 36 7 72529330 72529330 + Silent SNP T T C novel Unknown TCGA-25-1320-01 TCGA-25-1320-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 72529330 72529330 BAZ1B 7 T T C 56 YWHAG 7532 broad.mit.edu 36 7 75797405 75797405 + Missense_Mutation SNP G G A novel Unknown TCGA-25-1320-01 TCGA-25-1320-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 75797405 75797405 YWHAG 7 G G A 39 PPP1R3A 5506 broad.mit.edu 36 7 113305096 113305096 + Missense_Mutation SNP A A G novel Unknown TCGA-25-1320-01 TCGA-25-1320-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 113305096 113305096 PPP1R3A 7 A A G 4 MET 4233 broad.mit.edu 36 7 116127172 116127172 + Missense_Mutation SNP G G C novel Unknown TCGA-25-1320-01 TCGA-25-1320-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 116127172 116127172 MET 7 G G C 43 DOK2 9046 broad.mit.edu 36 8 21822857 21822857 + Missense_Mutation SNP C C A novel Unknown TCGA-25-1320-01 TCGA-25-1320-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 21822857 21822857 DOK2 8 C C A 17 CYP7B1 9420 broad.mit.edu 36 8 65690224 65690224 + Missense_Mutation SNP G G T novel Unknown TCGA-25-1320-01 TCGA-25-1320-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 65690224 65690224 CYP7B1 8 G G T 39 RECQL4 9401 broad.mit.edu 36 8 145708862 145708862 + Silent SNP G G C novel Unknown TCGA-25-1320-01 TCGA-25-1320-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 145708862 145708862 RECQL4 8 G G C 42 FOXB2 442425 broad.mit.edu 36 9 78824772 78824772 + Missense_Mutation SNP C C T novel Unknown TCGA-25-1320-01 TCGA-25-1320-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 78824772 78824772 FOXB2 9 C C T 26 FAM102A 399665 broad.mit.edu 36 9 129747626 129747626 + Missense_Mutation SNP G G A novel Unknown TCGA-25-1320-01 TCGA-25-1320-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 129747626 129747626 FAM102A 9 G G A 45 SURF1 6834 broad.mit.edu 36 9 135208769 135208769 + Silent SNP C C G novel Unknown TCGA-25-1320-01 TCGA-25-1320-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 135208769 135208769 SURF1 9 C C G 29 UBC 7316 broad.mit.edu 36 12 123963914 123963939 + Frame_Shift_Del DEL CAACCTCTGCTGGTCAGGAGGAATGC - CAACCTCTGCTGGTCAGGAGGAATGC novel Unknown TCGA-25-1320-01 TCGA-25-1320-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Del DEL 123963914 123963939 UBC 12 CAACCTCTGCTGGTCAGGAGGAATGC - CAACCTCTGCTGGTCAGGAGGAATGC 29 TP53 7157 broad.mit.edu 36 17 7520040 7520040 + Frame_Shift_Del DEL G - G novel Unknown TCGA-25-1320-01 TCGA-25-1320-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Del DEL 7520040 7520040 TP53 17 G - G 46 AATK 9625 broad.mit.edu 36 17 76707865 76707866 + In_Frame_Ins INS - GGGCGT - novel Unknown TCGA-25-1320-01 TCGA-25-1320-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad In_Frame_Ins INS 76707865 76707866 AATK 17 - GGGCGT - 27