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 KIAA0467 23334 broad.mit.edu 36 1 43671326 43671326 + Silent SNP G G A novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 43671326 43671326 KIAA0467 1 G G A 41 TMEM53 79639 broad.mit.edu 36 1 44892896 44892896 + Silent SNP G G A novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 44892896 44892896 TMEM53 1 G G A 40 FAM73A 374986 broad.mit.edu 36 1 78021524 78021524 + Missense_Mutation SNP C C A novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 78021524 78021524 FAM73A 1 C C A 26 GFI1 2672 broad.mit.edu 36 1 92721062 92721062 + Missense_Mutation SNP C C T novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 92721062 92721062 GFI1 1 C C T 23 GSTM1 2944 broad.mit.edu 36 1 110032380 110032381 + Missense_Mutation DNP GA GA TC novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation DNP 110032380 110032381 GSTM1 1 GA GA TC 37 KIF14 9928 broad.mit.edu 36 1 198789432 198789432 + Missense_Mutation SNP G G A novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 198789432 198789432 KIF14 1 G G A 42 AHCTF1 25909 broad.mit.edu 36 1 245146189 245146189 + Missense_Mutation SNP C C T novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 245146189 245146189 AHCTF1 1 C C T 32 MYST4 23522 broad.mit.edu 36 10 76454930 76454930 + Missense_Mutation SNP A A T novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 76454930 76454930 MYST4 10 A A T 7 PAAF1 80227 broad.mit.edu 36 11 73289042 73289042 + Missense_Mutation SNP T T A novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 73289042 73289042 PAAF1 11 T T A 51 PRMT8 56341 broad.mit.edu 36 12 3556335 3556335 + Missense_Mutation SNP C C G novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 3556335 3556335 PRMT8 12 C C G 30 MGAT4C 25834 broad.mit.edu 36 12 84901508 84901508 + Silent SNP G G A novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 84901508 84901508 MGAT4C 12 G G A 45 P2RX2 22953 broad.mit.edu 36 12 131708475 131708475 + Silent SNP C C A novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 131708475 131708475 P2RX2 12 C C A 26 JPH4 84502 broad.mit.edu 36 14 23110511 23110511 + Splice_Site_SNP SNP T T A novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Splice_Site_SNP SNP 23110511 23110511 JPH4 14 T T A 55 ZFYVE26 23503 broad.mit.edu 36 14 67322609 67322609 + Silent SNP A A C novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 67322609 67322609 ZFYVE26 14 A A C 13 SLC8A3 6547 broad.mit.edu 36 14 69703480 69703480 + Silent SNP G G A novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 69703480 69703480 SLC8A3 14 G G A 40 FMN1 342184 broad.mit.edu 36 15 30853848 30853848 + Splice_Site_SNP SNP C C G novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Splice_Site_SNP SNP 30853848 30853848 FMN1 15 C C G 32 SPATA5L1 79029 broad.mit.edu 36 15 43500544 43500544 + Silent SNP G G T novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 43500544 43500544 SPATA5L1 15 G G T 47 KIAA0174 9798 broad.mit.edu 36 16 70512211 70512211 + Silent SNP A A G novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 70512211 70512211 KIAA0174 16 A A G 9 TRPV1 7442 broad.mit.edu 36 17 3440376 3440376 + Missense_Mutation SNP C C T novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 3440376 3440376 TRPV1 17 C C T 18 TP53 7157 broad.mit.edu 36 17 7518275 7518275 + Missense_Mutation SNP C C T rs28934572 Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 7518275 7518275 TP53 17 C C T 26 LLGL1 3996 broad.mit.edu 36 17 18079297 18079297 + Silent SNP C C A novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 18079297 18079297 LLGL1 17 C C A 22 BRCA1 672 broad.mit.edu 36 17 38499782 38499782 + Nonsense_Mutation SNP A A C novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 38499782 38499782 BRCA1 17 A A C 13 PTGIR 5739 broad.mit.edu 36 19 51818885 51818885 + Silent SNP G G A novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 51818885 51818885 PTGIR 19 G G A 33 MYBPC2 4606 broad.mit.edu 36 19 55653989 55653989 + Missense_Mutation SNP C C A novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 55653989 55653989 MYBPC2 19 C C A 26 CACNG6 59285 broad.mit.edu 36 19 59193315 59193315 + Nonsense_Mutation SNP C C A novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 59193315 59193315 CACNG6 19 C C A 25 LILRA6 79168 broad.mit.edu 36 19 59436745 59436745 + Silent SNP G G T novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 59436745 59436745 LILRA6 19 G G T 41 RAB10 10890 broad.mit.edu 36 2 26203562 26203562 + Missense_Mutation SNP G G A novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 26203562 26203562 RAB10 2 G G A 45 CYP26B1 56603 broad.mit.edu 36 2 72224762 72224762 + Missense_Mutation SNP C C A novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 72224762 72224762 CYP26B1 2 C C A 26 BUB1 699 broad.mit.edu 36 2 111131611 111131611 + Missense_Mutation SNP T T C novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 111131611 111131611 BUB1 2 T T C 60 CLASP1 23332 broad.mit.edu 36 2 121935148 121935148 + Missense_Mutation SNP G G A novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 121935148 121935148 CLASP1 2 G G A 34 FIGN 55137 broad.mit.edu 36 2 164175267 164175267 + Missense_Mutation SNP G G T novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 164175267 164175267 FIGN 2 G G T 43 TTN 7273 broad.mit.edu 36 2 179112913 179112913 + Nonsense_Mutation SNP T T A novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 179112913 179112913 TTN 2 T T A 56 TTN 7273 broad.mit.edu 36 2 179357086 179357086 + Missense_Mutation SNP C C T novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 179357086 179357086 TTN 2 C C T 19 MPP4 58538 broad.mit.edu 36 2 202248210 202248210 + Missense_Mutation SNP G G A novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 202248210 202248210 MPP4 2 G G A 39 UBOX5 22888 broad.mit.edu 36 20 3050634 3050634 + Silent SNP C C T novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 3050634 3050634 UBOX5 20 C C T 25 ZNFX1 57169 broad.mit.edu 36 20 47298610 47298610 + Missense_Mutation SNP A A C novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 47298610 47298610 ZNFX1 20 A A C 9 ZNF70 7621 broad.mit.edu 36 22 22416478 22416478 + Missense_Mutation SNP G G C novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 22416478 22416478 ZNF70 22 G G C 33 EWSR1 2130 broad.mit.edu 36 22 28022304 28022304 + Missense_Mutation SNP A A G novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 28022304 28022304 EWSR1 22 A A G 6 ZNF621 285268 broad.mit.edu 36 3 40548885 40548885 + Missense_Mutation SNP A A G novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 40548885 40548885 ZNF621 3 A A G 16 HHATL 57467 broad.mit.edu 36 3 42713345 42713345 + Missense_Mutation SNP G G T novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 42713345 42713345 HHATL 3 G G T 34 MANF 7873 broad.mit.edu 36 3 51401519 51401519 + Missense_Mutation SNP A A C novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 51401519 51401519 MANF 3 A A C 13 ODAM 54959 broad.mit.edu 36 4 71098918 71098918 + Missense_Mutation SNP C C G novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 71098918 71098918 ODAM 4 C C G 29 PLAC8 51316 broad.mit.edu 36 4 84245198 84245198 + Splice_Site_SNP SNP C C A novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Splice_Site_SNP SNP 84245198 84245198 PLAC8 4 C C A 24 KIAA1109 84162 broad.mit.edu 36 4 123351629 123351629 + Missense_Mutation SNP G G C novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 123351629 123351629 KIAA1109 4 G G C 33 HEATR7B2 133558 broad.mit.edu 36 5 41068912 41068912 + Silent SNP A A T novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 41068912 41068912 HEATR7B2 5 A A T 5 TRIM36 55521 broad.mit.edu 36 5 114497487 114497487 + Silent SNP T T C novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 114497487 114497487 TRIM36 5 T T C 54 HSD17B4 3295 broad.mit.edu 36 5 118863133 118863133 + Missense_Mutation SNP A A G novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 118863133 118863133 HSD17B4 5 A A G 4 GRIA1 2890 broad.mit.edu 36 5 153170951 153170951 + Silent SNP G G A novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 153170951 153170951 GRIA1 5 G G A 41 GABRA6 2559 broad.mit.edu 36 5 161061197 161061197 + Missense_Mutation SNP C C T novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 161061197 161061197 GABRA6 5 C C T 24 HLA-G 3135 broad.mit.edu 36 6 29905575 29905575 + Missense_Mutation SNP A A C novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 29905575 29905575 HLA-G 6 A A C 7 DNAH8 1769 broad.mit.edu 36 6 38975645 38975645 + Missense_Mutation SNP A A C novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 38975645 38975645 DNAH8 6 A A C 7 GPR63 81491 broad.mit.edu 36 6 97353978 97353978 + Silent SNP G G A novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 97353978 97353978 GPR63 6 G G A 48 SYNE1 23345 broad.mit.edu 36 6 152632074 152632074 + Missense_Mutation SNP G G T novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 152632074 152632074 SYNE1 6 G G T 48 LPA 4018 broad.mit.edu 36 6 160897179 160897179 + Missense_Mutation SNP C C T novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 160897179 160897179 LPA 6 C C T 23 CARD11 84433 broad.mit.edu 36 7 2934793 2934793 + Silent SNP G G A novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 2934793 2934793 CARD11 7 G G A 37 CHPF2 54480 broad.mit.edu 36 7 150564433 150564433 + Missense_Mutation SNP C C A novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 150564433 150564433 CHPF2 7 C C A 25 PTPRN2 5799 broad.mit.edu 36 7 157566802 157566802 + Missense_Mutation SNP C C T novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 157566802 157566802 PTPRN2 7 C C T 20 NCAPG2 54892 broad.mit.edu 36 7 158168810 158168810 + Silent SNP G G A novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 158168810 158168810 NCAPG2 7 G G A 45 CSMD3 114788 broad.mit.edu 36 8 113427578 113427578 + Missense_Mutation SNP G G C novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 113427578 113427578 CSMD3 8 G G C 41 C5 727 broad.mit.edu 36 9 122778907 122778907 + Silent SNP G G C novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 122778907 122778907 C5 9 G G C 35 NTNG2 84628 broad.mit.edu 36 9 134063273 134063273 + Missense_Mutation SNP A A C novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 134063273 134063273 NTNG2 9 A A C 6 NOTCH1 4851 broad.mit.edu 36 9 138516325 138516325 + Silent SNP G G A novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 138516325 138516325 NOTCH1 9 G G A 40 ACRC 93953 broad.mit.edu 36 X 70741065 70741065 + Missense_Mutation SNP C C G novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 70741065 70741065 ACRC 23 C C G 18 COL4A5 1287 broad.mit.edu 36 X 107744884 107744885 + Missense_Mutation DNP GG GG AT novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation DNP 107744884 107744885 COL4A5 23 GG GG AT 43 AIFM1 9131 broad.mit.edu 36 X 129091276 129091276 + Missense_Mutation SNP C C G novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 129091276 129091276 AIFM1 23 C C G 24 FAM167B 84734 broad.mit.edu 36 1 32486679 32486684 + In_Frame_Del DEL GAGCTG - GAGCTG novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad In_Frame_Del DEL 32486679 32486684 FAM167B 1 GAGCTG - GAGCTG 37 ZNF573 126231 broad.mit.edu 36 19 42922720 42922721 + Frame_Shift_Ins INS - G - novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Ins INS 42922720 42922721 ZNF573 19 - G - 3 TBP 6908 broad.mit.edu 36 6 170712938 170712939 + In_Frame_Ins INS - CAG - novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad In_Frame_Ins INS 170712938 170712939 TBP 6 - CAG - 2 VPS13A 23230 broad.mit.edu 36 9 79086871 79086871 + Frame_Shift_Del DEL T - T novel Unknown TCGA-29-2427-01 TCGA-29-2427-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Del DEL 79086871 79086871 VPS13A 9 T - T 56