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 PANK4 55229 broad.mit.edu 36 1 2439497 2439497 + Missense_Mutation SNP T T A novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 2439497 2439497 PANK4 1 T T A 54 MMEL1 79258 broad.mit.edu 36 1 2515210 2515210 + Missense_Mutation SNP C C A novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 2515210 2515210 MMEL1 1 C C A 28 ZBTB17 7709 broad.mit.edu 36 1 16146090 16146090 + Silent SNP G G C novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 16146090 16146090 ZBTB17 1 G G C 35 CSMD2 114784 broad.mit.edu 36 1 33771391 33771391 + Silent SNP C C T novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 33771391 33771391 CSMD2 1 C C T 27 MTF1 4520 broad.mit.edu 36 1 38078292 38078292 + Silent SNP G G A novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 38078292 38078292 MTF1 1 G G A 46 LEPRE1 64175 broad.mit.edu 36 1 42986028 42986028 + Missense_Mutation SNP C C T novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 42986028 42986028 LEPRE1 1 C C T 31 GLIS1 148979 broad.mit.edu 36 1 53744907 53744908 + Missense_Mutation DNP GT GT TG novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation DNP 53744907 53744908 GLIS1 1 GT GT TG 48 C1orf85 112770 broad.mit.edu 36 1 154531311 154531311 + Missense_Mutation SNP C C T novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 154531311 154531311 C1orf85 1 C C T 18 FCRL5 83416 broad.mit.edu 36 1 155757585 155757585 + Silent SNP A A G novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 155757585 155757585 FCRL5 1 A A G 9 HSD17B7 51478 broad.mit.edu 36 1 161039937 161039937 + Silent SNP G G A novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 161039937 161039937 HSD17B7 1 G G A 39 PM20D1 148811 broad.mit.edu 36 1 204081137 204081137 + Missense_Mutation SNP C C G novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 204081137 204081137 PM20D1 1 C C G 22 MUC6 4588 broad.mit.edu 36 11 1008575 1008575 + Missense_Mutation SNP G G T novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 1008575 1008575 MUC6 11 G G T 39 KCNQ1 3784 broad.mit.edu 36 11 2825597 2825597 + Missense_Mutation SNP G G C novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 2825597 2825597 KCNQ1 11 G G C 42 OR51S1 119692 broad.mit.edu 36 11 4826625 4826625 + Silent SNP C C G novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 4826625 4826625 OR51S1 11 C C G 22 OR2AG2 338755 broad.mit.edu 36 11 6745955 6745955 + Missense_Mutation SNP T T G novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 6745955 6745955 OR2AG2 11 T T G 56 NUP160 23279 broad.mit.edu 36 11 47826390 47826390 + Silent SNP G G A novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 47826390 47826390 NUP160 11 G G A 38 OR5D14 219436 broad.mit.edu 36 11 55320009 55320009 + Silent SNP T T C novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 55320009 55320009 OR5D14 11 T T C 49 INTS5 80789 broad.mit.edu 36 11 62172743 62172743 + Missense_Mutation SNP A A G novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 62172743 62172743 INTS5 11 A A G 15 ATG2A 23130 broad.mit.edu 36 11 64431868 64431870 + Missense_Mutation TNP CTG CTG TCA novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation TNP 64431868 64431870 ATG2A 11 CTG CTG TCA 28 PITPNM1 9600 broad.mit.edu 36 11 67022229 67022230 + Missense_Mutation DNP GC GC TG novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation DNP 67022229 67022230 PITPNM1 11 GC GC TG 42 SIDT2 51092 broad.mit.edu 36 11 116557414 116557414 + Missense_Mutation SNP C C A novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 116557414 116557414 SIDT2 11 C C A 21 BACE1 23621 broad.mit.edu 36 11 116691544 116691544 + Missense_Mutation SNP A A G novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 116691544 116691544 BACE1 11 A A G 3 ABCB9 23457 broad.mit.edu 36 12 121980614 121980614 + Missense_Mutation SNP G G A novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 121980614 121980614 ABCB9 12 G G A 39 CENPJ 55835 broad.mit.edu 36 13 24378632 24378632 + Missense_Mutation SNP G G T novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 24378632 24378632 CENPJ 13 G G T 48 PCDH17 27253 broad.mit.edu 36 13 57107191 57107191 + Missense_Mutation SNP C C A novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 57107191 57107191 PCDH17 13 C C A 18 KLHL1 57626 broad.mit.edu 36 13 69579662 69579662 + Silent SNP G G A novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 69579662 69579662 KLHL1 13 G G A 45 TNFSF13B 10673 broad.mit.edu 36 13 107720506 107720506 + Missense_Mutation SNP G G C novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 107720506 107720506 TNFSF13B 13 G G C 38 ALKBH1 8846 broad.mit.edu 36 14 77230865 77230865 + Missense_Mutation SNP C C T novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 C T C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 77230865 77230865 ALKBH1 14 C C T 32 PLCB2 5330 broad.mit.edu 36 15 38368263 38368263 + Missense_Mutation SNP A A C novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 38368263 38368263 PLCB2 15 A A C 7 WDR90 197335 broad.mit.edu 36 16 643656 643657 + Missense_Mutation DNP TT TT CC novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation DNP 643656 643657 WDR90 16 TT TT CC 60 RNPS1 10921 broad.mit.edu 36 16 2245709 2245709 + Missense_Mutation SNP C C A novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 2245709 2245709 RNPS1 16 C C A 32 PAQR4 124222 broad.mit.edu 36 16 2961897 2961898 + Missense_Mutation DNP GG GG CT novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation DNP 2961897 2961898 PAQR4 16 GG GG CT 39 KATNB1 10300 broad.mit.edu 36 16 56344611 56344611 + Missense_Mutation SNP T T G novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 56344611 56344611 KATNB1 16 T T G 55 METT10D 79066 broad.mit.edu 36 17 2270377 2270377 + Silent SNP G G A novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 2270377 2270377 METT10D 17 G G A 39 OR3A1 4994 broad.mit.edu 36 17 3141985 3141985 + Missense_Mutation SNP C C T novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 3141985 3141985 OR3A1 17 C C T 21 CHRNB1 1140 broad.mit.edu 36 17 7289199 7289199 + Missense_Mutation SNP T T C novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 7289199 7289199 CHRNB1 17 T T C 55 KCNH6 81033 broad.mit.edu 36 17 58955404 58955404 + Silent SNP G G T novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 58955404 58955404 KCNH6 17 G G T 38 ANKRD12 23253 broad.mit.edu 36 18 9198762 9198762 + Missense_Mutation SNP G G A novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 9198762 9198762 ANKRD12 18 G G A 42 SMAD7 4092 broad.mit.edu 36 18 44730313 44730313 + Nonsense_Mutation SNP G G T novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 44730313 44730313 SMAD7 18 G G T 46 SMARCA4 6597 broad.mit.edu 36 19 11005525 11005526 + Missense_Mutation DNP AG AG CA novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation DNP 11005525 11005526 SMARCA4 19 AG AG CA 11 AKAP8 10270 broad.mit.edu 36 19 15344906 15344906 + Missense_Mutation SNP C C A novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 15344906 15344906 AKAP8 19 C C A 27 ANO8 57719 broad.mit.edu 36 19 17301630 17301630 + Missense_Mutation SNP A A T novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 17301630 17301630 ANO8 19 A A T 10 KCNN1 3780 broad.mit.edu 36 19 17945992 17945992 + Missense_Mutation SNP C C G novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 17945992 17945992 KCNN1 19 C C G 28 NUDT19 390916 broad.mit.edu 36 19 37875230 37875231 + Missense_Mutation DNP CG CG AC novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation DNP 37875230 37875231 NUDT19 19 CG CG AC 23 IRGQ 126298 broad.mit.edu 36 19 48789034 48789034 + Missense_Mutation SNP T T G novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 48789034 48789034 IRGQ 19 T T G 59 FCAR 2204 broad.mit.edu 36 19 60092891 60092891 + Missense_Mutation SNP C C T novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 60092891 60092891 FCAR 19 C C T 31 BRSK1 84446 broad.mit.edu 36 19 60505999 60505999 + Missense_Mutation SNP G G A novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 60505999 60505999 BRSK1 19 G G A 42 NLRP5 126206 broad.mit.edu 36 19 61230253 61230253 + Missense_Mutation SNP C C T rs45627733 Unknown TCGA-04-1342-01 TCGA-04-1342-11 C T C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 61230253 61230253 NLRP5 19 C C T 19 STON1-GTF2A1L 286749 broad.mit.edu 36 2 48727389 48727389 + Missense_Mutation SNP G G A rs61754876 Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 48727389 48727389 STON1-GTF2A1L 2 G G A 40 SNRNP200 23020 broad.mit.edu 36 2 96321311 96321311 + Missense_Mutation SNP G G A novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 96321311 96321311 SNRNP200 2 G G A 39 CNNM3 26505 broad.mit.edu 36 2 96846657 96846658 + Missense_Mutation DNP AA AA CT novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation DNP 96846657 96846658 CNNM3 2 AA AA CT 5 MARS2 92935 broad.mit.edu 36 2 198279841 198279841 + Missense_Mutation SNP G G T novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 198279841 198279841 MARS2 2 G G T 42 SLCO4A1 28231 broad.mit.edu 36 20 60768244 60768244 + Missense_Mutation SNP G G C novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 60768244 60768244 SLCO4A1 20 G G C 42 DGCR2 9993 broad.mit.edu 36 22 17406556 17406556 + Missense_Mutation SNP C C A novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 17406556 17406556 DGCR2 22 C C A 27 LZTR1 8216 broad.mit.edu 36 22 19666711 19666712 + Missense_Mutation DNP AG AG CA novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation DNP 19666711 19666712 LZTR1 22 AG AG CA 7 MICALL1 85377 broad.mit.edu 36 22 36650624 36650624 + Nonsense_Mutation SNP G G T novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 36650624 36650624 MICALL1 22 G G T 37 CHKB 1120 broad.mit.edu 36 22 49364798 49364799 + Nonsense_Mutation DNP CA CA AC novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation DNP 49364798 49364799 CHKB 22 CA CA AC 25 GRIP2 80852 broad.mit.edu 36 3 14511477 14511477 + Missense_Mutation SNP G G A novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 14511477 14511477 GRIP2 3 G G A 38 SCN10A 6336 broad.mit.edu 36 3 38777222 38777222 + Nonsense_Mutation SNP G G A novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 38777222 38777222 SCN10A 3 G G A 38 LAMB2 3913 broad.mit.edu 36 3 49136172 49136172 + Missense_Mutation SNP C C T novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 49136172 49136172 LAMB2 3 C C T 30 BSN 8927 broad.mit.edu 36 3 49663128 49663128 + Missense_Mutation SNP C C T novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 49663128 49663128 BSN 3 C C T 23 ZNF721 170960 broad.mit.edu 36 4 426638 426638 + Nonsense_Mutation SNP G G A novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 426638 426638 ZNF721 4 G G A 48 WHSC2 7469 broad.mit.edu 36 4 1955019 1955019 + Missense_Mutation SNP C C A novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 1955019 1955019 WHSC2 4 C C A 25 RAB28 9364 broad.mit.edu 36 4 12992272 12992272 + Missense_Mutation SNP G G A novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 12992272 12992272 RAB28 4 G G A 40 KIT 3815 broad.mit.edu 36 4 55299419 55299419 + Missense_Mutation SNP T T C novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 T C T T Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 55299419 55299419 KIT 4 T T C 50 UGT2B17 7367 broad.mit.edu 36 4 69116706 69116706 + Missense_Mutation SNP G G A novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 69116706 69116706 UGT2B17 4 G G A 48 SLC12A7 10723 broad.mit.edu 36 5 1129888 1129889 + Nonsense_Mutation DNP CC CC GT novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation DNP 1129888 1129889 SLC12A7 5 CC CC GT 26 MTRR 4552 broad.mit.edu 36 5 7950055 7950055 + Missense_Mutation SNP G G T novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 7950055 7950055 MTRR 5 G G T 43 ANKRD32 84250 broad.mit.edu 36 5 94056760 94056760 + Missense_Mutation SNP T T C novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 94056760 94056760 ANKRD32 5 T T C 51 WDR36 134430 broad.mit.edu 36 5 110474532 110474532 + Missense_Mutation SNP A A G novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 110474532 110474532 WDR36 5 A A G 8 CAMK4 814 broad.mit.edu 36 5 110847627 110847627 + Missense_Mutation SNP C C A novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 C A C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 110847627 110847627 CAMK4 5 C C A 27 REEP2 51308 broad.mit.edu 36 5 137802824 137802824 + Missense_Mutation SNP G G A novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 137802824 137802824 REEP2 5 G G A 44 PCDHA11 56138 broad.mit.edu 36 5 140229831 140229831 + Missense_Mutation SNP A A G novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 140229831 140229831 PCDHA11 5 A A G 7 PCDHB14 56122 broad.mit.edu 36 5 140584797 140584797 + Missense_Mutation SNP C C G novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 140584797 140584797 PCDHB14 5 C C G 18 SH3PXD2B 285590 broad.mit.edu 36 5 171698541 171698541 + Missense_Mutation SNP A A C novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 171698541 171698541 SH3PXD2B 5 A A C 9 KCND2 3751 broad.mit.edu 36 7 119702804 119702804 + Silent SNP C C G novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 119702804 119702804 KCND2 7 C C G 32 FEZF1 389549 broad.mit.edu 36 7 121730470 121730470 + Silent SNP C C T novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 121730470 121730470 FEZF1 7 C C T 27 GDF6 392255 broad.mit.edu 36 8 97241878 97241878 + Silent SNP G G A novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 97241878 97241878 GDF6 8 G G A 40 PLEC 5339 broad.mit.edu 36 8 145078380 145078380 + Missense_Mutation SNP C C T novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 145078380 145078380 PLEC 8 C C T 23 S1PR3 1903 broad.mit.edu 36 9 90806932 90806932 + Missense_Mutation SNP G G C novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 90806932 90806932 S1PR3 9 G G C 37 C9orf129 445577 broad.mit.edu 36 9 95121273 95121273 + Missense_Mutation SNP T T G novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 95121273 95121273 C9orf129 9 T T G 57 PAPPA 5069 broad.mit.edu 36 9 118104947 118104947 + Missense_Mutation SNP C C G novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 C G C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 118104947 118104947 PAPPA 9 C C G 19 TLR4 7099 broad.mit.edu 36 9 119515072 119515072 + Missense_Mutation SNP A A G novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 A G A A Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 119515072 119515072 TLR4 9 A A G 4 C9orf16 79095 broad.mit.edu 36 9 129965712 129965712 + Silent SNP C C G novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 129965712 129965712 C9orf16 9 C C G 24 C9orf114 51490 broad.mit.edu 36 9 130629169 130629169 + Missense_Mutation SNP C C T novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 130629169 130629169 C9orf114 9 C C T 29 L1CAM 3897 broad.mit.edu 36 X 152783059 152783059 + Nonsense_Mutation SNP C C T novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 C T C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Nonsense_Mutation SNP 152783059 152783059 L1CAM 23 C C T 22 WDR81 124997 broad.mit.edu 36 17 1578265 1578271 + Frame_Shift_Del DEL GGGCTCT - - novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Del DEL 1578265 1578271 WDR81 17 GGGCTCT - - 39 MCM5 4174 broad.mit.edu 36 22 34147330 34147332 + In_Frame_Del DEL CGC - CGC novel Unknown TCGA-04-1342-01 TCGA-04-1342-11 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad In_Frame_Del DEL 34147330 34147332 MCM5 22 CGC - CGC 27