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	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	ACHILLES_Lineage_Results_Top_Genes	CGC_CancerGermlineMut	CGC_CancerMolecularGenetics	CGC_CancerSomaticMut	CGC_CancerSyndrome	CGC_Chr	CGC_ChrBand	CGC_GeneID	CGC_Name	CGC_OtherGermlineMut	CGC_TissueType	COSMIC_n_overlapping_mutations	COSMIC_overlapping_mutation_descriptions	ClinVar_ASSEMBLY	ClinVar_HGMD_ID	ClinVar_SYM	ClinVar_TYPE	ClinVar_rs	Ensembl_so_accession	Ensembl_so_term	Familial_Cancer_Genes_Reference	Familial_Cancer_Genes_Synonym	annotation_transcript	bcgsc	broad	build	ccds_id	dbNSFP_1000Gp1_AC	dbNSFP_1000Gp1_AF	dbNSFP_1000Gp1_AFR_AC	dbNSFP_1000Gp1_AFR_AF	dbNSFP_1000Gp1_AMR_AC	dbNSFP_1000Gp1_AMR_AF	dbNSFP_1000Gp1_ASN_AC	dbNSFP_1000Gp1_ASN_AF	dbNSFP_1000Gp1_EUR_AC	dbNSFP_1000Gp1_EUR_AF	dbNSFP_Ancestral_allele	dbNSFP_CADD_phred	dbNSFP_CADD_raw	dbNSFP_CADD_raw_rankscore	dbNSFP_ESP6500_AA_AF	dbNSFP_ESP6500_EA_AF	dbNSFP_Ensembl_geneid	dbNSFP_Ensembl_transcriptid	dbNSFP_FATHMM_pred	dbNSFP_FATHMM_rankscore	dbNSFP_FATHMM_score	dbNSFP_GERP_NR	dbNSFP_GERP_RS	dbNSFP_GERP_RS_rankscore	dbNSFP_Interpro_domain	dbNSFP_LRT_Omega	dbNSFP_LRT_converted_rankscore	dbNSFP_LRT_pred	dbNSFP_LRT_score	dbNSFP_LR_pred	dbNSFP_LR_rankscore	dbNSFP_LR_score	dbNSFP_MutationAssessor_pred	dbNSFP_MutationAssessor_rankscore	dbNSFP_MutationAssessor_score	dbNSFP_MutationTaster_converted_rankscore	dbNSFP_MutationTaster_pred	dbNSFP_MutationTaster_score	dbNSFP_Polyphen2_HDIV_pred	dbNSFP_Polyphen2_HDIV_rankscore	dbNSFP_Polyphen2_HDIV_score	dbNSFP_Polyphen2_HVAR_pred	dbNSFP_Polyphen2_HVAR_rankscore	dbNSFP_Polyphen2_HVAR_score	dbNSFP_RadialSVM_pred	dbNSFP_RadialSVM_rankscore	dbNSFP_RadialSVM_score	dbNSFP_Reliability_index	dbNSFP_SIFT_converted_rankscore	dbNSFP_SIFT_pred	dbNSFP_SIFT_score	dbNSFP_SLR_test_statistic	dbNSFP_SiPhy_29way_logOdds	dbNSFP_SiPhy_29way_logOdds_rankscore	dbNSFP_SiPhy_29way_pi	dbNSFP_UniSNP_ids	dbNSFP_Uniprot_aapos	dbNSFP_Uniprot_acc	dbNSFP_Uniprot_id	dbNSFP_aaalt	dbNSFP_aapos	dbNSFP_aapos_FATHMM	dbNSFP_aapos_SIFT	dbNSFP_aaref	dbNSFP_cds_strand	dbNSFP_codonpos	dbNSFP_folddegenerate	dbNSFP_genename	dbNSFP_hg18_pos1coor	dbNSFP_phastCons100way_vertebrate	dbNSFP_phastCons100way_vertebrate_rankscore	dbNSFP_phastCons46way_placental	dbNSFP_phastCons46way_placental_rankscore	dbNSFP_phastCons46way_primate	dbNSFP_phastCons46way_primate_rankscore	dbNSFP_phyloP100way_vertebrate	dbNSFP_phyloP100way_vertebrate_rankscore	dbNSFP_phyloP46way_placental	dbNSFP_phyloP46way_placental_rankscore	dbNSFP_phyloP46way_primate	dbNSFP_phyloP46way_primate_rankscore	dbNSFP_refcodon	entrez_gene_id	external_id_capture	gencode_transcript_name	gencode_transcript_status	gencode_transcript_tags	gencode_transcript_type	gene_type	havana_transcript	hgsc	igv_bad	ucsc	t_alt_count	t_ref_count	n_alt_count	n_ref_count	validation_judgement_rna	validation_power_rna	validation_tumor_alt_count_rna	validation_tumor_ref_count_rna	validation_normal_alt_count_rna	validation_normal_ref_count_rna	min_val_count_rna	validation_judgement_targeted	validation_power_targeted	validation_tumor_alt_count_targeted	validation_tumor_ref_count_targeted	validation_normal_alt_count_targeted	validation_normal_ref_count_targeted	min_val_count_targeted	validation_judgement_localAssembly	validation_power_localAssembly	t_alt_count_localAssembly	t_ref_count_localAssembly	n_alt_count_localAssembly	n_ref_count_localAssembly	min_val_count_localAssembly	validation_judgement_KRAS	validation_power_KRAS	t_alt_count_KRAS	t_ref_count_KRAS	n_alt_count_KRAS	n_ref_count_KRAS	min_val_count_KRAS	pon_loglike	pon_pass_loglike	localAssembly_detected	ExAC_AN	ExAC_AC	ExAC_LQ	passExAC	SCNA_NA	SCNA_NB	SCNA_q_hat	SCNA_tau	IS_SCNA	purity	ploidy	dna_fraction_in_tumor	CCF_hat	CCF_CI95_low	CCF_CI95_high	CCF_mode	CCF_mean	CCF_median	clonal	CCF_CI_low	CCF_CI_high
NRAP	4892	broad.mit.edu	37	10	115374049	115374049	+	Missense_Mutation	SNP	A	A	G			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr10:115374049A>G	ENST00000359988.3	-	29	3437	c.3193T>C	c.(3193-3195)Tac>Cac	p.Y1065H	NRAP_ENST00000369360.3_Missense_Mutation_p.Y1038H|NRAP_ENST00000369358.4_Missense_Mutation_p.Y1073H|NRAP_ENST00000360478.3_Missense_Mutation_p.Y1030H	NM_001261463.1|NM_198060.3	NP_001248392.1|NP_932326.2			nebulin-related anchoring protein			95		Colorectal(252;0.0233)|Breast(234;0.188)			GCCTCTTTGTATTTGTACTAA	0.453000																								0							SO:0001583	missense			ENST00000359988.3	0	1	hg19	CCDS7579.1	.	.	.	.	.	.	.	.	.	.	A	22.500000	4.298801	0.810250	.	.	ENSG00000197893	ENST00000369358;ENST00000369360;ENST00000359988;ENST00000360478	D;D;D;D	0.99958	-9.03;-9.03;-9.03;-9.03	5.650000	5.650000	0.869990	.	0.000000	0.85682	D	0.000000	D	0.99955	0.9981	M	0.89601	3.045	0.485710	D	0.999672	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.999	D	0.95382	0.8474	10	0.87932	D	0	.	15.876100	0.791620	1.0:0.0:0.0:0.0	.	1065;1030;1065	A0AVL2;Q86VF7-4;Q86VF7	.;.;NRAP_HUMAN	H	1073;1038;1065;1030	ENSP00000358365:Y1073H;ENSP00000358367:Y1038H;ENSP00000353078:Y1065H;ENSP00000353666:Y1030H	ENSP00000353078:Y1065H	Y	-	1	0	NRAP	115364039	1	0.714170	1	0.803570	0.999000	0.989320	8.290000	0.899250	2.153000	0.673060	0.528000	0.532280	TAC		TCGA-IB-7897-01A-21D-2201-08	NRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050425.2	0	0	0	12	751	0	113		0	0	0	0	113	2		0	0	0	0	0	2	1	9.990121e-01	12	737	0	114	2		0	0	0	0	113	2	-3.225686	1	1	0	0		1	0	1	1	1.996160	0	0.160000	2	0.155949	0.190000	0.100000	0.330000	0.200000	0.209900	0.190000	0	0.140000	0.260000
TUB	7275	broad.mit.edu	37	11	8123100	8123100	+	Silent	SNP	G	G	A	rs147880022	byFrequency	TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr11:8123100G>A	ENST00000299506.2	+	12	1604	c.1455G>A	c.(1453-1455)ccG>ccA	p.P485P	TUB_ENST00000305253.4_Silent_p.P540P|TUB_ENST00000534099.1_Silent_p.P491P	NM_177972.2	NP_813977.1	P50607	TUB_HUMAN	tubby bipartite transcription factor			26		all_lung(207;6.91e-20)|Lung NSC(207;3.36e-17)			ACAACTACCCGCTGTGTGCAC	0.582000																								0							SO:0001819	synonymous_variant			ENST00000299506.2	0	1	hg19	CCDS7787.1																																																																																				TCGA-IB-7897-01A-21D-2201-08	TUB-003	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385823.1	0	0	0	21	725	1	100	0	7.176845e-02	0	15	1	100	2		0	0	0	0	0	2	0	4.178368e-01	20	715	1	100	23		0	0	0	1	100	2	-2.747571	1	1	121412	46	49	1	0	1	1	1.998490	0	0.160000	2	0.156627	0.350000	0.220000	0.510000	0.350000	0.363537	0.350000	0	0.280000	0.440000
KRAS	3845	broad.mit.edu	37	12	25398284	25398284	+	Missense_Mutation	SNP	C	C	T	rs121913529		TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	KRAS_deep			Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr12:25398284C>T	ENST00000256078.4	-	2	98	c.35G>A	c.(34-36)gGt>gAt	p.G12D	KRAS_ENST00000556131.1_Missense_Mutation_p.G12D|KRAS_ENST00000557334.1_Missense_Mutation_p.G12D|KRAS_ENST00000311936.3_Missense_Mutation_p.G12D	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	25349	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)		GCCTACGCCACCAGCTCCAAC	0.348000	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		pancreatic, colorectal, lung, thyroid, AML, others				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)			Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		L, E, M, O	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)						SO:0001583	missense	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	ENST00000256078.4			hg19	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	23.400000	4.409094	0.833400	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19	5.680000	5.680000	0.881260	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.85919	0.5809	M	0.91818	3.245	0.807220	D	1.000000	B;P	0.35714	0.385;0.517	B;B	0.41619	0.257;0.361	D	0.87870	0.2670	10	0.87932	D	0	.	18.371900	0.904090	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	D	12	ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D	ENSP00000256078:G12D	G	-	2	0	KRAS	25289551	1	0.714170	1	0.803570	0.998000	0.957120	7.743000	0.850200	2.668000	0.907890	0.563000	0.778840	GGT		TCGA-IB-7897-01A-21D-2201-08	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1		0		1	173	0	20	1	9.654497e-02	5	37	0	20	2	1	7.486278e-01	8	351	0	255	2		0	0	0	0	0	2	1	9.986617e-01	96	7928	0	20	2	-3.039667	1	1	121404	2	44	1	1	2	3	2.001917	0	0.160000	2	0.163347	0.110000	0.010000	1.000000	0.070000	0.172109	0.110000	0	0.040000	0.250000
AKAP3	10566	broad.mit.edu	37	12	4737445	4737445	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr12:4737445C>A	ENST00000545990.2	-	5	1147	c.623G>T	c.(622-624)aGt>aTt	p.S208I	RP11-500M8.7_ENST00000536588.1_Intron|AKAP3_ENST00000228850.1_Missense_Mutation_p.S208I	NM_001278309.1	NP_001265238.1	O75969	AKAP3_HUMAN	A kinase (PRKA) anchor protein 3			51					ATTTGGGGGACTTTGTGATGA	0.488000																								0							SO:0001583	missense			ENST00000545990.2	0	1	hg19	CCDS8531.1	.	.	.	.	.	.	.	.	.	.	C	4.255000	0.046299	0.082430	.	.	ENSG00000111254	ENST00000228850;ENST00000545990	T;T	0.10668	2.85;2.85	4.610000	-1.240000	0.094350	A-kinase anchor 110kDa, C-terminal (1);	0.765712	0.12130	N	0.496807	T	0.09335	0.0230	L	0.57536	1.79	0.093100	N	1.000000	B	0.12630	0.006	B	0.12837	0.008	T	0.37663	-0.9696	10	0.87932	D	0	.	1.390100	0.022490	0.303:0.3889:0.1314:0.1767	.	208	O75969	AKAP3_HUMAN	I	208	ENSP00000228850:S208I;ENSP00000440994:S208I	ENSP00000228850:S208I	S	-	2	0	AKAP3	4607706	0	0.058580	0	0.037020	0.019000	0.099040	-0.674000	0.052330	-0.341000	0.083760	-0.459000	0.054220	AGT		TCGA-IB-7897-01A-21D-2201-08	AKAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398911.2	0	0	0	9	613	0	106	0	3.156426e-02	0	17	0	106	2		0	0	0	0	0	2	1	9.937834e-01	9	603	0	106	2		0	0	0	0	106	2	-6.999037	1	0	0	0		1	1	2	3	2.034411	0	0.160000	2	0.170616	0.200000	0.090000	1.000000	0.180000	0.301733	0.200000	0	0.130000	0.330000
LRP1	4035	broad.mit.edu	37	12	57587450	57587450	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr12:57587450G>A	ENST00000243077.3	+	47	8252	c.7786G>A	c.(7786-7788)Gac>Aac	p.D2596N	MIR1228_ENST00000408438.1_RNA	NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1			184				Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	GGATGGCTCTGACGAGATCCC	0.622000																								0							SO:0001583	missense			ENST00000243077.3	1	1	hg19	CCDS8932.1	.	.	.	.	.	.	.	.	.	.	G	14.420000	2.529304	0.449690	.	.	ENSG00000123384	ENST00000243077	D	0.99214	-5.57	5.010000	4.100000	0.479360	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.000000	0.64402	D	0.000001	D	0.99594	0.9853	H	0.97214	3.96	0.807220	D	1.000000	D	0.69078	0.997	D	0.83275	0.996	D	0.97659	1.0159	10	0.59425	D	0.04	.	12.951700	0.584050	0.0821:0.0:0.9179:0.0	.	2596	Q07954	LRP1_HUMAN	N	2596	ENSP00000243077:D2596N	ENSP00000243077:D2596N	D	+	1	0	LRP1	55873717	1	0.714170	1.000000e-01	0.211370	0.069000	0.166280	7.767000	0.853310	2.606000	0.881270	0.655000	0.942530	GAC		TCGA-IB-7897-01A-21D-2201-08	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	0	0	0	13	422	0	56	1	9.998884e-01	3	531	0	56	2		0	0	0	0	0	2	1	9.994651e-01	12	413	0	56	2		0	0	0	0	56	2	-12.209560	1	1	0	0		1	1	2	3	2.048807	0	0.160000	2	0.177760	0.420000	0.220000	1.000000	0.370000	0.517308	0.420000	0	0.300000	1.000000
LTBR	4055	broad.mit.edu	37	12	6494502	6494502	+	Missense_Mutation	SNP	G	G	T			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr12:6494502G>T	ENST00000228918.4	+	4	755	c.429G>T	c.(427-429)gaG>gaT	p.E143D	LTBR_ENST00000543190.1_Missense_Mutation_p.E36D|LTBR_ENST00000539925.1_Missense_Mutation_p.E124D|LTBR_ENST00000541102.1_Missense_Mutation_p.E36D	NM_002342.2	NP_002333.1	P36941	TNR3_HUMAN	lymphotoxin beta receptor (TNFR superfamily, member 3)			15					CACACTGCGAGCTACTTTCTG	0.607000																								0							SO:0001583	missense			ENST00000228918.4	0	1	hg19	CCDS8544.1	.	.	.	.	.	.	.	.	.	.	G	13.660000	2.303124	0.407950	.	.	ENSG00000111321	ENST00000539925;ENST00000228918;ENST00000540343;ENST00000536876;ENST00000543190;ENST00000541102	T;T;T;T;T	0.73047	0.12;0.12;0.12;-0.71;0.12	4.790000	1.890000	0.256350	TNFR/CD27/30/40/95 cysteine-rich region (1);	0.432883	0.23340	N	0.049255	T	0.78227	0.4250	M	0.69358	2.11	0.093100	N	0.999996	D;D;D	0.76494	0.996;0.993;0.999	D;D;D	0.76071	0.986;0.967;0.987	T	0.66913	-0.5803	9	.	.	.	-1.2798	6.562500	0.224930	0.1755:0.0:0.6788:0.1457	.	124;124;143	F5GXE7;B7Z1D2;P36941	.;.;TNR3_HUMAN	D	124;143;36;138;36;36	ENSP00000440875:E124D;ENSP00000228918:E143D;ENSP00000437647:E138D;ENSP00000438955:E36D;ENSP00000438605:E36D	.	E	+	3	2	LTBR	6364763	7.490000e-01	0.283050	7.600000e-02	0.202970	0.307000	0.278230	0.698000	0.255710	-0.127000	0.116610	-1.134000	0.019550	GAG		TCGA-IB-7897-01A-21D-2201-08	LTBR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399422.1	0	0	1	6	338	0	45	1	9.671553e-01	44	306	0	45	2		0	0	0	0	0	2	1	9.613008e-01	6	326	0	42	2		0	0	0	0	45	2	-6.478423	1	1	0	0		1	1	2	3	2.034411	0	0.160000	2	0.170616	0.250000	0.090000	1.000000	0.220000	0.346511	0.250000	0	0.160000	0.440000
CHD4	1108	broad.mit.edu	37	12	6686950	6686950	+	Splice_Site	SNP	C	C	T			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr12:6686950C>T	ENST00000357008.2	-	37	5525		c.e37+1		CHD4_ENST00000544484.1_Splice_Site|CHD4_ENST00000309577.6_Splice_Site|CHD4_ENST00000544040.1_Splice_Site|RP5-940J5.6_ENST00000501075.2_RNA	NM_001273.2	NP_001264.2	Q14839	CHD4_HUMAN	chromodomain helicase DNA binding protein 4	p.?(3)		2					CAACCGCTCACCTTAAACCTT	0.463000													Colon(32;586 792 4568 16848 45314)											3	Unknown(3)						SO:0001630	splice_region_variant			ENST00000357008.2	0	1	hg19	CCDS8552.1	.	.	.	.	.	.	.	.	.	.	C	25.200000	4.616076	0.873590	.	.	ENSG00000111642	ENST00000544484;ENST00000544040;ENST00000309577;ENST00000357008;ENST00000537464	.	.	.	5.510000	5.510000	0.819320	.	.	.	.	.	.	.	.	.	.	.	0.807220	D	1.000000	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.785900	0.964370	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CHD4	6557211	1	0.714170	1	0.803570	0.922000	0.554780	7.464000	0.808870	2.746000	0.941840	0.655000	0.942530	.		TCGA-IB-7897-01A-21D-2201-08	CHD4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		0	0	0	11	845	0	122	1	4.209928e-03	2	5	0	122	2	1	8.221828e-01	4	241	0	152	2	1	9.981142e-01	11	826	0	122	2		0	0	0	0	122	2	-7.260967	1	0	0	0		1	1	2	3	2.034411	0	0.160000	2	0.170616	0.170000	0.080000	1.000000	0.170000	0.279661	0.170000	0	0.120000	0.280000
CLEC4A	50856	broad.mit.edu	37	12	8276535	8276535	+	Missense_Mutation	SNP	A	A	G			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr12:8276535A>G	ENST00000229332.5	+	1	308	c.61A>G	c.(61-63)Atc>Gtc	p.I21V	CLEC4A_ENST00000345999.3_Missense_Mutation_p.I21V|CLEC4A_ENST00000352620.3_Missense_Mutation_p.I21V|CLEC4A_ENST00000360500.3_Missense_Mutation_p.I21V	NM_016184.3|NM_194447.2|NM_194450.2	NP_057268.1|NP_919429.2|NP_919432.1	Q9UMR7	CLC4A_HUMAN	C-type lectin domain family 4, member A			11					GTCCTCAGGCATCAACACAGC	0.418000																								0							SO:0001583	missense			ENST00000229332.5	0	1	hg19	CCDS8590.1	.	.	.	.	.	.	.	.	.	.	A	5.547000	0.285885	0.105130	.	.	ENSG00000111729	ENST00000229332;ENST00000345999;ENST00000352620;ENST00000360500;ENST00000546339	T;T;T;T;T	0.44083	5.49;5.5;5.33;5.33;0.93	4.070000	-0.299000	0.128080	.	.	.	.	.	T	0.26882	0.0658	L	0.43152	1.355	0.093100	N	1.000000	B;B;B;P	0.36990	0.32;0.048;0.32;0.577	B;B;B;B	0.31442	0.058;0.024;0.129;0.13	T	0.11842	-1.0571	9	0.27785	T	0.31	.	5.520600	0.169310	0.5456:0.3515:0.1029:0.0	.	21;21;21;21	Q9UMR7-3;Q9UMR7-4;Q9UMR7-2;Q9UMR7	.;.;.;CLC4A_HUMAN	V	21;21;21;21;10	ENSP00000229332:I21V;ENSP00000344646:I21V;ENSP00000247243:I21V;ENSP00000353690:I21V;ENSP00000443082:I10V	ENSP00000229332:I21V	I	+	1	0	CLEC4A	8167802	0	0.058580	0	0.037020	0.011000	0.076110	-0.061000	0.116930	-0.051000	0.133340	0.528000	0.532280	ATC		TCGA-IB-7897-01A-21D-2201-08	CLEC4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400257.1	0	0	0	8	448	0	58	0	2.581110e-01	0	50	0	58	2		0	0	0	0	0	2	1	9.888124e-01	7	442	0	57	2		0	0	0	0	58	2	-7.503095	1	1	121412	2	35	1	1	2	3	2.034411	0	0.160000	2	0.170616	0.240000	0.100000	1.000000	0.220000	0.340927	0.240000	0	0.160000	0.410000
NALCN	259232	broad.mit.edu	37	13	101755619	101755619	+	Silent	SNP	G	G	A			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr13:101755619G>A	ENST00000251127.6	-	26	3042	c.2961C>T	c.(2959-2961)gtC>gtT	p.V987V		NM_052867.2	NP_443099.1	Q8IZF0	NALCN_HUMAN	sodium leak channel, non-selective			177	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)				GGCACCGAAGGACCATTAGAA	0.443000																								0							SO:0001819	synonymous_variant			ENST00000251127.6	1	1	hg19	CCDS9498.1																																																																																				TCGA-IB-7897-01A-21D-2201-08	NALCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045663.2	0	0	0	14	614	0	84	0	1.058279e-01	0	23	0	84	2		0	0	0	0	0	2	1	9.997110e-01	14	599	0	82	2		0	0	0	0	84	2	-3.390712	1	1	0	0		1	0	1	1	1.998708	0	0.160000	2	0.156627	0.280000	0.150000	0.440000	0.270000	0.293889	0.280000	0	0.210000	0.370000
KLHDC4	54758	broad.mit.edu	37	16	87790046	87790046	+	Nonsense_Mutation	SNP	C	C	A			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr16:87790046C>A	ENST00000270583.5	-	3	287	c.229G>T	c.(229-231)Gag>Tag	p.E77*	KLHDC4_ENST00000353170.5_Intron|KLHDC4_ENST00000347925.5_Nonsense_Mutation_p.E77*	NM_017566.3	NP_060036.2	Q8TBB5	KLDC4_HUMAN	kelch domain containing 4			21					AGGATTAACTCATCTTTCTCA	0.438000																								0							SO:0001587	stop_gained			ENST00000270583.5	0	1	hg19	CCDS10963.1	.	.	.	.	.	.	.	.	.	.	C	36.000000	5.966446	0.971560	.	.	ENSG00000104731	ENST00000270583;ENST00000347925	.	.	.	5.180000	5.180000	0.714440	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.807220	A	1.000000	.	.	.	.	.	.	.	.	.	.	0.30078	T	0.28	-15.5645	15.853900	0.789600	0.0:1.0:0.0:0.0	.	.	.	.	X	77	.	ENSP00000270583:E77X	E	-	1	0	KLHDC4	86347547	1	0.714170	9.980000e-01	0.565050	0.925000	0.559040	7.019000	0.764120	2.417000	0.820170	0.655000	0.942530	GAG		TCGA-IB-7897-01A-21D-2201-08	KLHDC4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269109.2	0	0	0	7	316	0	48	0	1.721969e-01	0	30	0	48	2		0	0	0	0	0	2	1	9.802506e-01	7	313	0	48	2		0	0	0	0	48	2	-7.256089	1	1	0	0		1	1	2	3	2.009794	0	0.160000	2	0.165342	0.290000	0.120000	1.000000	0.270000	0.349561	0.290000	0	0.190000	0.450000
KRT26	353288	broad.mit.edu	37	17	38928255	38928255	+	Silent	SNP	C	C	T			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr17:38928255C>T	ENST00000335552.4	-	1	159	c.111G>A	c.(109-111)tcG>tcA	p.S37S		NM_181539.4	NP_853517.2			keratin 26			16		Breast(137;0.00526)			TTCTTGCTCCCGATCCAACAC	0.557000																								0							SO:0001819	synonymous_variant			ENST00000335552.4	0	1	hg19	CCDS11374.1																																																																																				TCGA-IB-7897-01A-21D-2201-08	KRT26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257215.1	0	0	0	15	1181	0	166		0	0	0	0	166	2		0	0	0	0	0	2	1	9.998441e-01	16	1155	0	163	2		0	0	0	0	166	2	-1.774740	0	1	121412	3	40	1	0	1	1	1.997116	0	0.160000	2	0.155949	0.150000	0.080000	0.250000	0.160000	0.165394	0.150000	0	0.110000	0.200000
VEZF1	7716	broad.mit.edu	37	17	56060697	56060697	+	Missense_Mutation	SNP	G	G	T			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr17:56060697G>T	ENST00000581208.1	-	2	131	c.91C>A	c.(91-93)Ctg>Atg	p.L31M	VEZF1_ENST00000584396.1_Missense_Mutation_p.L22M	NM_007146.2	NP_009077.2	Q14119	VEZF1_HUMAN	vascular endothelial zinc finger 1			10					GCAGAGCTCAGGAGGGGCAGC	0.498000																								0							SO:0001583	missense			ENST00000581208.1	0	1	hg19	CCDS32687.1	.	.	.	.	.	.	.	.	.	.	G	15.130000	2.741196	0.491510	.	.	ENSG00000136451	ENST00000258963	.	.	.	5.940000	5.940000	0.961940	.	0.000000	0.85682	D	0.000000	T	0.61751	0.2372	L	0.27053	0.805	0.807220	D	1.000000	D	0.65815	0.995	P	0.61874	0.895	T	0.63102	-0.6712	9	0.59425	D	0.04	-1.2014	13.558900	0.617770	0.0706:0.0:0.9294:0.0	.	31	Q14119	VEZF1_HUMAN	M	31	.	ENSP00000258963:L31M	L	-	1	2	VEZF1	53415696	1	0.714170	1	0.803570	0.998000	0.957120	5.455000	0.666580	2.823000	0.971560	0.643000	0.837060	CTG		TCGA-IB-7897-01A-21D-2201-08	VEZF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443321.1	0	0	0	14	944	0	128	1	5.631268e-01	7	117	0	128	2		0	0	0	0	0	2	1	9.996863e-01	14	913	0	129	2		0	0	0	0	128	2	-2.523497	1	1	0	0		1	1	2	3	2.009361	0	0.160000	2	0.165342	0.190000	0.100000	1.000000	0.180000	0.247287	0.190000	0	0.140000	0.260000
RPTOR	57521	broad.mit.edu	37	17	78914377	78914377	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr17:78914377C>A	ENST00000306801.3	+	25	3363	c.3001C>A	c.(3001-3003)Cag>Aag	p.Q1001K	CTD-2561B21.4_ENST00000576032.1_RNA|RPTOR_ENST00000575542.1_3'UTR|RPTOR_ENST00000544334.2_Missense_Mutation_p.Q843K	NM_020761.2	NP_065812.1	Q8N122	RPTOR_HUMAN	regulatory associated protein of MTOR, complex 1			44					TGTCAGGAGGCAGGCCCAGCA	0.632000																								0							SO:0001583	missense			ENST00000306801.3	0	1	hg19	CCDS11773.1	.	.	.	.	.	.	.	.	.	.	C	21.500000	4.165535	0.783390	.	.	ENSG00000141564	ENST00000306801;ENST00000544334	T;T	0.41758	1.01;0.99	4.800000	4.800000	0.616430	.	0.070570	0.64402	D	0.000019	T	0.56804	0.2010	L	0.50333	1.59	0.807220	D	1.000000	P;B	0.43578	0.811;0.111	P;B	0.57846	0.828;0.026	T	0.55173	-0.8182	10	0.42905	T	0.14	.	17.850400	0.887460	0.0:1.0:0.0:0.0	.	843;1001	F5H7J5;Q8N122	.;RPTOR_HUMAN	K	1001;843	ENSP00000307272:Q1001K;ENSP00000442479:Q843K	ENSP00000307272:Q1001K	Q	+	1	0	RPTOR	76528972	1	0.714170	9.620000e-01	0.402830	0.334000	0.286980	6.977000	0.761410	2.209000	0.713650	0.561000	0.740990	CAG		TCGA-IB-7897-01A-21D-2201-08	RPTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438125.1	0	0	0	4	125	0	17	0	4.948841e-01	0	45	0	17	2		0	0	0	0	0	2	1	8.878568e-01	4	123	0	17	2		0	0	0	0	17	2	-7.273564	1	0	0	0		1	1	2	3	2.009361	0	0.160000	2	0.165342	0.440000	0.150000	1.000000	0.390000	0.494581	0.440000	0	0.260000	0.730000
UQCR11	10975	broad.mit.edu	37	19	1605381	1605381	+	Missense_Mutation	SNP	A	A	G			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr19:1605381A>G	ENST00000591899.3	-	1	99	c.28T>C	c.(28-30)Tac>Cac	p.Y10H	UQCR11_ENST00000593029.1_5'UTR|UQCR11_ENST00000585937.1_Missense_Mutation_p.Y10H|UQCR11_ENST00000585671.1_Missense_Mutation_p.Y10H|UQCR11_ENST00000589880.1_Missense_Mutation_p.Y10H	NM_006830.3	NP_006821.1	O14957	QCR10_HUMAN	ubiquinol-cytochrome c reductase, complex III subunit XI			5					AGCTCCCGGTAGCGTGGGCCC	0.731000																								0							SO:0001583	missense			ENST00000591899.3	0	1	hg19	CCDS12073.1	.	.	.	.	.	.	.	.	.	.	A	16.300000	3.083359	0.558610	.	.	ENSG00000127540	ENST00000262946	.	.	.	4.760000	4.760000	0.606890	.	0.169791	0.39083	N	0.001465	T	0.62539	0.2436	.	.	.	0.327630	N	0.504898	D	0.59767	0.986	P	0.60541	0.876	T	0.68903	-0.5286	8	0.28530	T	0.3	-13.3155	12.135200	0.539660	1.0:0.0:0.0:0.0	.	10	O14957	QCR10_HUMAN	H	10	.	ENSP00000262946:Y10H	Y	-	1	0	UQCR11	1556381	9.900000e-01	0.363640	9.700000e-01	0.415380	0.042000	0.138120	4.876000	0.630790	2.002000	0.586370	0.533000	0.621200	TAC		TCGA-IB-7897-01A-21D-2201-08	UQCR11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449668.3	0	0	0	3	71	0	11	0	7.061626e-01	0	55	0	11	2		0	0	0	0	0	2	1	7.945735e-01	2	68	0	11	2		0	0	0	0	11	2	-6.985544	1	0	0	0		1	1	2	3	2.019232	0	0.160000	2	0.167328	0.600000	0.170000	1.000000	1.000000	0.632819	0.600000	0	0.340000	1.000000
MAP1S	55201	broad.mit.edu	37	19	17838243	17838243	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr19:17838243G>A	ENST00000324096.4	+	5	2201	c.2050G>A	c.(2050-2052)Gca>Aca	p.A684T	CTD-3149D2.4_ENST00000595363.1_RNA|MAP1S_ENST00000544059.2_Missense_Mutation_p.A658T|MAP1S_ENST00000597681.1_3'UTR	NM_018174.4	NP_060644.4	Q66K74	MAP1S_HUMAN	microtubule-associated protein 1S			25					CTCACTACCCGCAGAGGTGGG	0.711000																								0							SO:0001583	missense			ENST00000324096.4	0	1	hg19	CCDS32954.1	.	.	.	.	.	.	.	.	.	.	G	16.430000	3.120183	0.566130	.	.	ENSG00000130479	ENST00000324096;ENST00000544059	T;T	0.24350	1.86;1.87	4.160000	3.110000	0.358120	.	0.000000	0.49916	D	0.000137	T	0.43344	0.1243	L	0.61218	1.895	0.301450	N	0.803570	D;D	0.89917	1.0;1.0	D;D	0.72338	0.977;0.975	T	0.38779	-0.9645	10	0.46703	T	0.11	-18.582	10.018800	0.420310	0.1039:0.0:0.8961:0.0	.	658;684	B4DH53;Q66K74	.;MAP1S_HUMAN	T	684;658	ENSP00000325313:A684T;ENSP00000439243:A658T	ENSP00000325313:A684T	A	+	1	0	MAP1S	17699243	1	0.714170	7.000000e-03	0.137880	0.236000	0.253710	7.147000	0.773820	0.855000	0.353590	0.484000	0.476210	GCA		TCGA-IB-7897-01A-21D-2201-08	MAP1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466027.1	0	0	0	3	63	0	12	0	2.246807e-01	0	15	0	12	2		0	0	0	0	0	2	1	8.125546e-01	3	63	0	12	2		0	0	0	0	12	2	-6.837779	1	1	0	0		1	1	2	3	2.019232	0	0.160000	2	0.167328	0.670000	0.190000	1.000000	1.000000	0.679057	0.670000	0	0.370000	1.000000
FCGBP	8857	broad.mit.edu	37	19	40398010	40398010	+	Silent	SNP	G	G	A			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr19:40398010G>A	ENST00000221347.6	-	14	6964	c.6957C>T	c.(6955-6957)gcC>gcT	p.A2319A		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein			165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)		GGGCCCCAGCGGCCTGACAGG	0.652000																								0							SO:0001819	synonymous_variant			ENST00000221347.6	0	1	hg19	CCDS12546.1																																																																																				TCGA-IB-7897-01A-21D-2201-08	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	0	0	0	14	304	0	44		0	0	0	0	44	2		0	0	0	0	0	2	1	9.995947e-01	13	280	0	70	2		0	0	0	0	44	2	-15.308550	1	1	111138	3	32	1	1	2	3	2.019232	0	0.160000	2	0.167328	0.580000	0.320000	1.000000	0.550000	0.618611	0.580000	0	0.430000	0.800000
PNMAL2	57469	broad.mit.edu	37	19	46998201	46998201	+	Silent	SNP	G	G	C			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr19:46998201G>C	ENST00000377655.2	-	1	521	c.522C>G	c.(520-522)acC>acG	p.T174T	PNMAL2_ENST00000594749.1_Intron|PNMAL2_ENST00000599531.1_Silent_p.T174T|AC011484.1_ENST00000377652.3_Missense_Mutation_p.W104C			Q9ULN7	PNML2_HUMAN	paraneoplastic Ma antigen family-like 2			8		Ovarian(192;0.00965)|all_neural(266;0.0459)			TGCCCTTCTGGGTCAACCTGT	0.647000																								0							SO:0001819	synonymous_variant			ENST00000377655.2	0	1	hg19		.	.	.	.	.	.	.	.	.	.	G	13.410000	2.229867	0.393990	.	.	ENSG00000204850	ENST00000377652	.	.	.	2.830000	-0.738000	0.111250	.	.	.	.	.	T	0.34658	0.0905	.	.	.	0.525010	D	0.999953	D	0.56968	0.978	B	0.42030	0.373	T	0.29701	-1.0003	7	0.87932	D	0	-1.6491	3.125200	0.064050	0.2934:0.2286:0.478:0.0	.	104	Q6ZVU4	.	C	104	.	ENSP00000366880:W104C	W	+	3	0	AC011484.1	51690041	5.760000e-01	0.267000	6.260000e-01	0.292130	0.859000	0.490530	-0.415000	0.071060	-0.071000	0.128860	-0.424000	0.059670	TGG		TCGA-IB-7897-01A-21D-2201-08	PNMAL2-201	KNOWN	basic	protein_coding	protein_coding		0	0	0	10	647	0	134	0	2.045703e-02	0	13	0	134	2		0	0	0	0	0	2	1	9.963332e-01	10	625	0	130	2		0	0	0	0	134	2	-2.543759	1	1	0	0		1	1	2	3	2.019232	0	0.160000	2	0.167328	0.200000	0.090000	1.000000	0.190000	0.279209	0.200000	0	0.140000	0.300000
FEM1A	55527	broad.mit.edu	37	19	4793864	4793864	+	Silent	SNP	C	C	A			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr19:4793864C>A	ENST00000269856.3	+	1	2137	c.1998C>A	c.(1996-1998)atC>atA	p.I666I	AC005523.2_ENST00000596170.1_RNA|AC005523.3_ENST00000598782.1_lincRNA|AC005523.2_ENST00000601192.1_RNA	NM_018708.2	NP_061178.1	Q9BSK4	FEM1A_HUMAN	fem-1 homolog a (C. elegans)			17		Hepatocellular(1079;0.137)			AGGCGTTCATCGAACTGCACT	0.592000																								0							SO:0001819	synonymous_variant			ENST00000269856.3	0	1	hg19	CCDS12135.1																																																																																				TCGA-IB-7897-01A-21D-2201-08	FEM1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459000.1	0	0	0	3	91	0	17	0	7.911232e-01	0	88	0	17	2		0	0	0	0	0	2	1	8.021710e-01	3	88	0	17	2		0	0	0	0	17	2	-6.428781	1	1	0	0		1	1	2	3	2.019232	0	0.160000	2	0.167328	0.480000	0.130000	1.000000	1.000000	0.537298	0.480000	0	0.270000	0.870000
PUSL1	126789	broad.mit.edu	37	1	1244619	1244619	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr1:1244619G>A	ENST00000379031.5	+	3	366	c.289G>A	c.(289-291)Gcc>Acc	p.A97T	PUSL1_ENST00000470520.1_3'UTR|ACAP3_ENST00000354700.5_5'Flank|CPSF3L_ENST00000462432.1_5'Flank|ACAP3_ENST00000353662.3_5'Flank	NM_153339.1	NP_699170.1	Q8N0Z8	PUSL1_HUMAN	pseudouridylate synthase-like 1			5	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)			CCTGGCCGAGGCCCTCAACAC	0.746000																								0							SO:0001583	missense			ENST00000379031.5	0	1	hg19	CCDS20.1	.	.	.	.	.	.	.	.	.	.	g	16.090000	3.025366	0.546830	.	.	ENSG00000169972	ENST00000379031	T	0.56275	0.47	4.630000	2.500000	0.302970	Pseudouridine synthase I, TruA, N-terminal (1);Pseudouridine synthase, catalytic domain (1);Pseudouridine synthase I, TruA, alpha/beta domain (1);	0.420768	0.18516	N	0.138901	T	0.73032	0.3535	M	0.90922	3.16	0.329240	D	0.516194	D	0.63880	0.993	P	0.61070	0.883	T	0.82554	-0.0399	10	0.87932	D	0	-24.0168	12.158200	0.540890	0.0:0.2825:0.7175:0.0	.	97	Q8N0Z8	PUSL1_HUMAN	T	97	ENSP00000368318:A97T	ENSP00000368318:A97T	A	+	1	0	PUSL1	1234482	9.750000e-01	0.340420	9.710000e-01	0.417170	0.211000	0.244170	2.775000	0.477020	2.141000	0.664460	0.450000	0.298270	GCC		TCGA-IB-7897-01A-21D-2201-08	PUSL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009438.1	0	0	0	3	40	0	10		0	0	0	0	10	2		0	0	0	0	0	2	1	8.051028e-01	2	40	0	10	2		0	0	0	0	10	2	-8.098799	1	0	0	0		1	1	2	3	2.023424	0	0.160000	2	0.167987	0.980000	0.290000	1.000000	1.000000	0.832256	0.980000	1	0.560000	1.000000
ACBD6	84320	broad.mit.edu	37	1	180461444	180461444	+	Missense_Mutation	SNP	A	A	G			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr1:180461444A>G	ENST00000367595.3	-	3	1031	c.344T>C	c.(343-345)aTc>aCc	p.I115T		NM_032360.3	NP_115736.1	Q9BR61	ACBD6_HUMAN	acyl-CoA binding domain containing 6		ACBD6/RRP15(2)	7					AACTACTGCGATATATTCCTG	0.358000																								0							SO:0001583	missense			ENST00000367595.3	1	1	hg19	CCDS1339.1	.	.	.	.	.	.	.	.	.	.	A	18.530000	3.645038	0.673580	.	.	ENSG00000135847	ENST00000367595	T	0.33654	1.4	5.050000	5.050000	0.679360	FERM/acyl-CoA-binding protein, 3-helical bundle (1);Acyl-CoA-binding protein, ACBP (4);	0.228453	0.45126	D	0.000387	T	0.54159	0.1841	M	0.78223	2.4	0.499150	D	0.999832	B	0.28026	0.198	P	0.45712	0.491	T	0.57533	-0.7795	10	0.51188	T	0.08	-8.125	13.795600	0.631680	1.0:0.0:0.0:0.0	.	115	Q9BR61	ACBD6_HUMAN	T	115	ENSP00000356567:I115T	ENSP00000356567:I115T	I	-	2	0	ACBD6	178728067	1	0.714170	9.610000e-01	0.401460	0.726000	0.416060	6.617000	0.742100	1.903000	0.550910	0.528000	0.532280	ATC		TCGA-IB-7897-01A-21D-2201-08	ACBD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084998.1	0	0	0	11	485	0	51	1	8.257995e-01	8	135	0	51	2		0	0	0	0	0	2	1	9.979724e-01	10	467	0	51	2		0	0	0	0	51	2	-9.696806	1	1	0	0		1	1	2	3	2.009767	0	0.160000	2	0.165342	0.290000	0.150000	1.000000	0.280000	0.345086	0.290000	0	0.210000	0.410000
PINK1	65018	broad.mit.edu	37	1	20975596	20975596	+	Missense_Mutation	SNP	T	T	G			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr1:20975596T>G	ENST00000321556.4	+	7	1454	c.1360T>G	c.(1360-1362)Tac>Gac	p.Y454D	PINK1-AS_ENST00000451424.1_RNA|PINK1_ENST00000492302.1_3'UTR	NM_032409.2	NP_115785.1	Q9BXM7	PINK1_HUMAN	PTEN induced putative kinase 1			14		all_lung(284;2.72e-05)|Lung NSC(340;2.94e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000147)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)			CAATCCCTTCTACGGCCAGGG	0.607000													Esophageal Squamous(145;853 1803 8146 34412 35011)											0							SO:0001583	missense			ENST00000321556.4	0	1	hg19	CCDS211.1	.	.	.	.	.	.	.	.	.	.	T	20.400000	3.986271	0.745890	.	.	ENSG00000158828	ENST00000321556	T	0.64260	-0.09	6.050000	6.050000	0.981690	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.057544	0.64402	D	0.000001	T	0.72922	0.3521	L	0.45470	1.425	0.807220	D	1.000000	D;D	0.89917	1.0;1.0	D;D	0.87578	0.993;0.998	T	0.74225	-0.3734	10	0.56958	D	0.05	-10.0039	12.991800	0.586220	0.0:0.0:0.0:1.0	.	147;454	Q9BXM7-2;Q9BXM7	.;PINK1_HUMAN	D	454	ENSP00000364204:Y454D	ENSP00000364204:Y454D	Y	+	1	0	PINK1	20848183	1	0.714170	9.700000e-01	0.415380	0.633000	0.380330	7.179000	0.776650	2.323000	0.785720	0.533000	0.621200	TAC		TCGA-IB-7897-01A-21D-2201-08	PINK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007954.1	0	0	0	5	243	0	43	1	9.518734e-01	8	264	0	43	2		0	0	0	0	0	2	1	9.319124e-01	4	235	0	43	2		0	0	0	0	43	2	-7.034824	1	0	0	0		1	1	2	3	2.013505	0	0.160000	2	0.166005	0.280000	0.100000	1.000000	0.250000	0.347252	0.280000	0	0.170000	0.460000
SLC35F3	148641	broad.mit.edu	37	1	234454518	234454518	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr1:234454518G>A	ENST00000366617.3	+	5	997	c.769G>A	c.(769-771)Ggc>Agc	p.G257S	SLC35F3_ENST00000366618.3_Missense_Mutation_p.G326S			Q8IY50	S35F3_HUMAN	solute carrier family 35, member F3			32	Ovarian(103;0.0454)	all_cancers(173;0.145)|Prostate(94;0.0885)	OV - Ovarian serous cystadenocarcinoma(106;0.00531)		GCTCCTCCTGGGCAGTGCTAA	0.468000																								0							SO:0001583	missense			ENST00000366617.3	0	1	hg19		.	.	.	.	.	.	.	.	.	.	G	36.000000	5.759291	0.968980	.	.	ENSG00000183780	ENST00000366618;ENST00000366617	T;T	0.73469	-0.75;-0.75	5.710000	5.710000	0.891250	.	0.000000	0.85682	D	0.000000	D	0.87736	0.6252	M	0.83483	2.645	0.807220	D	1.000000	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.86546	0.1831	10	0.40728	T	0.16	-24.7144	19.855900	0.967580	0.0:0.0:1.0:0.0	.	257;326	Q8IY50;Q8IY50-2	S35F3_HUMAN;.	S	326;257	ENSP00000355577:G326S;ENSP00000355576:G257S	ENSP00000355576:G257S	G	+	1	0	SLC35F3	232521141	1	0.714170	1	0.803570	0.999000	0.989320	9.869000	0.998100	2.693000	0.918960	0.655000	0.942530	GGC		TCGA-IB-7897-01A-21D-2201-08	SLC35F3-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000128322.1	0	0	0	15	1015	0	141	0	1.045027e-01	0	35	0	141	2		0	0	0	0	0	2	1	9.998431e-01	15	991	0	139	2		0	0	0	0	141	2	-2.240007	0	1	0	0		1	1	2	3	2.009767	0	0.160000	2	0.165342	0.180000	0.100000	1.000000	0.180000	0.245936	0.180000	0	0.140000	0.260000
GREM2	64388	broad.mit.edu	37	1	240656720	240656720	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr1:240656720G>A	ENST00000318160.4	-	2	322	c.56C>T	c.(55-57)gCg>gTg	p.A19V		NM_022469.3	NP_071914.3	Q9H772	GREM2_HUMAN	gremlin 2, DAN family BMP antagonist			10		all_cancers(173;0.0196)	OV - Ovarian serous cystadenocarcinoma(106;0.0123)		CCGGGCTTCCGCCACCTTCAC	0.612000																								0							SO:0001583	missense			ENST00000318160.4	0	1	hg19	CCDS31070.1	.	.	.	.	.	.	.	.	.	.	G	17.330000	3.361699	0.614030	.	.	ENSG00000180875	ENST00000318160	T	0.32753	1.44	5.150000	3.220000	0.369610	.	0.235752	0.35378	U	0.003251	T	0.22205	0.0535	L	0.38175	1.15	0.405520	D	0.981126	B	0.27971	0.196	B	0.16722	0.016	T	0.04708	-1.0932	10	0.48119	T	0.1	-3.9963	10.411000	0.442940	0.0:0.1461:0.7017:0.1522	.	19	Q9H772	GREM2_HUMAN	V	19	ENSP00000318650:A19V	ENSP00000318650:A19V	A	-	2	0	GREM2	238723343	4.110000e-01	0.253840	8.180000e-01	0.326260	0.995000	0.863560	3.465000	0.530640	0.524000	0.285020	0.557000	0.710580	GCG		TCGA-IB-7897-01A-21D-2201-08	GREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096286.1	0	0	0	7	167	0	27	0	4.024150e-02	0	7	0	27	2		0	0	0	0	0	2	1	9.706459e-01	5	148	0	25	2		0	0	0	0	27	2	-9.404836	1	0	121222	22	41	1	1	2	3	2.009767	0	0.160000	2	0.165342	0.540000	0.240000	1.000000	1.000000	0.581787	0.540000	0	0.360000	0.810000
PHACTR4	65979	broad.mit.edu	37	1	28807088	28807088	+	Silent	SNP	C	C	A			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr1:28807088C>A	ENST00000373839.3	+	9	1993	c.1732C>A	c.(1732-1734)Cgg>Agg	p.R578R	PHACTR4_ENST00000373836.3_Silent_p.R588R|PHACTR4_ENST00000493669.1_3'UTR|RNU6ATAC27P_ENST00000408289.1_RNA	NM_001048183.1	NP_001041648.1	Q8IZ21	PHAR4_HUMAN	phosphatase and actin regulator 4			32		Colorectal(325;3.46e-05)|Lung NSC(340;4.37e-05)|all_lung(284;7.01e-05)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)			GAATGAAATACGGCACCAGAT	0.428000																								0							SO:0001819	synonymous_variant			ENST00000373839.3	1	1	hg19	CCDS41293.1																																																																																				TCGA-IB-7897-01A-21D-2201-08	PHACTR4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000009868.4	0	0	0	29	1319	0	202	1	5.938299e-01	6	85	0	202	2		0	0	0	0	0	2	1	1	28	1287	0	201	2		0	0	0	0	202	2	-2.237376	0	1	0	0		1	1	2	3	2.008535	0	0.160000	2	0.165342	0.270000	0.180000	1.000000	0.270000	0.324927	0.270000	0	0.220000	0.340000
CYB5RL	606495	broad.mit.edu	37	1	54640404	54640404	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr1:54640404C>T	ENST00000534324.1	-	6	835	c.836G>A	c.(835-837)tGc>tAc	p.C279Y	RP11-446E24.4_ENST00000311841.7_Intron|CYB5RL_ENST00000419823.2_Missense_Mutation_p.C279Y|CYB5RL_ENST00000401046.3_Missense_Mutation_p.C131Y|CYB5RL_ENST00000542737.1_Missense_Mutation_p.C279Y|AL357673.1_ENST00000536061.1_5'Flank|CYB5RL_ENST00000287899.8_Missense_Mutation_p.C211Y|CYB5RL_ENST00000537208.1_Missense_Mutation_p.C211Y|RP11-446E24.4_ENST00000525949.1_5'Flank			Q6IPT4	NB5R5_HUMAN	cytochrome b5 reductase-like			8					TCTCCGACAGCAGCTGACCAG	0.552000																								0							SO:0001583	missense			ENST00000534324.1	1	1	hg19	CCDS44151.1	.	.	.	.	.	.	.	.	.	.	C	7.486000	0.649652	0.145160	.	.	ENSG00000215883	ENST00000419823;ENST00000401046;ENST00000534324;ENST00000287899;ENST00000542737;ENST00000537208	D;D;D;D;D;D	0.85861	-2.04;-2.04;-2.04;-1.9;-2.04;-1.9	5.140000	3.210000	0.368540	Oxidoreductase FAD/NAD(P)-binding (1);	0.413252	0.17337	U	0.177898	T	0.77356	0.4118	L	0.36672	1.1	0.243540	N	0.994901	B;B	0.22414	0.069;0.001	B;B	0.28553	0.091;0.001	T	0.64219	-0.6459	10	0.32370	T	0.25	-19.4038	7.849600	0.294460	0.0:0.2439:0.6084:0.1477	.	279;131	Q6IPT4;Q6IPT4-3	NB5R5_HUMAN;.	Y	279;131;279;211;279;211	ENSP00000409075:C279Y;ENSP00000383825:C131Y;ENSP00000434343:C279Y;ENSP00000287899:C211Y;ENSP00000438151:C279Y;ENSP00000443797:C211Y	ENSP00000287899:C211Y	C	-	2	0	CYB5RL	54412992	9.840000e-01	0.351630	4.650000e-01	0.271550	0.376000	0.300140	2.109000	0.418630	0.696000	0.316960	0.555000	0.697020	TGC		TCGA-IB-7897-01A-21D-2201-08	CYB5RL-010	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388318.1	0	0	0	8	234	0	38	0	6.308051e-02	0	11	0	38	2		0	0	0	0	0	2	1	9.871359e-01	7	222	0	37	2		0	0	0	0	38	2	-9.592363	1	1	0	0		1	1	2	3	2.008535	0	0.160000	2	0.165342	0.440000	0.200000	1.000000	0.410000	0.489363	0.440000	0	0.300000	0.650000
TMPRSS3	64699	broad.mit.edu	37	21	43796648	43796648	+	Splice_Site	SNP	A	A	T			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr21:43796648A>T	ENST00000291532.3	-	11	2150		c.e11+1		TMPRSS3_ENST00000474596.1_Splice_Site|TMPRSS3_ENST00000380399.1_Splice_Site|TMPRSS3_ENST00000433957.2_Splice_Site|TMPRSS3_ENST00000398405.1_Splice_Site	NM_032404.2	NP_115780.1	P57727	TMPS3_HUMAN	transmembrane protease, serine 3			13					GCGGCCCCGTACCTGGCAGCT	0.622000											OREG0031642	type=REGULATORY REGION|TFbs=ESR1|Dataset=Estrogen Receptor Alpha Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)												0							SO:0001630	splice_region_variant			ENST00000291532.3	0	1	hg19	CCDS13686.1	.	.	.	.	.	.	.	.	.	.	A	22.700000	4.329752	0.816900	.	.	ENSG00000160183	ENST00000291532;ENST00000433957;ENST00000398405;ENST00000380399	.	.	.	4.940000	4.940000	0.650670	.	.	.	.	.	.	.	.	.	.	.	0.807220	D	1.000000	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.599700	0.684320	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TMPRSS3	42669717	1	0.714170	9.450000e-01	0.383650	0.866000	0.496080	8.554000	0.906890	1.840000	0.535000	0.482000	0.462540	.		TCGA-IB-7897-01A-21D-2201-08	TMPRSS3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195347.1	0	0	0	9	451	0	84	0	0	1	0	0	84	2		0	0	0	0	0	2	1	9.934552e-01	9	438	0	83	2		0	0	0	0	84	2	-8.500725	1	1	0	0		1	0	1	1	1.998541	0	0.160000	2	0.156627	0.250000	0.120000	0.440000	0.240000	0.266331	0.250000	0	0.170000	0.340000
C2orf71	388939	broad.mit.edu	37	2	29295748	29295748	+	Silent	SNP	C	C	T			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr2:29295748C>T	ENST00000331664.5	-	1	1379	c.1380G>A	c.(1378-1380)ggG>ggA	p.G460G		NM_001029883.2	NP_001025054.1	A6NGG8	CB071_HUMAN	chromosome 2 open reading frame 71			60					AGACCCCAATCCCAAAGGAAT	0.557000																								0							SO:0001819	synonymous_variant			ENST00000331664.5	0	1	hg19	CCDS42669.1																																																																																				TCGA-IB-7897-01A-21D-2201-08	C2orf71-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324924.3	0	0	0	16	535	0	92		0	0	0	0	92	2		0	0	0	0	0	2	1	9.999178e-01	15	521	0	91	2		0	0	0	0	92	2	-3.452277	1	1	0	0		1	1	2	3	2.012100	0	0.160000	2	0.166005	0.380000	0.220000	1.000000	0.360000	0.428343	0.380000	0	0.290000	0.510000
SCN5A	6331	broad.mit.edu	37	3	38591931	38591931	+	Missense_Mutation	SNP	C	C	G			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr3:38591931C>G	ENST00000333535.4	-	28	6081	c.5932G>C	c.(5932-5934)Gac>Cac	p.D1978H	SCN5A_ENST00000450102.2_Missense_Mutation_p.D1924H|SCN5A_ENST00000451551.2_Missense_Mutation_p.D1924H|SCN5A_ENST00000413689.1_Missense_Mutation_p.D1978H|SCN5A_ENST00000423572.2_Missense_Mutation_p.D1977H|SCN5A_ENST00000455624.2_Missense_Mutation_p.D1945H|SCN5A_ENST00000443581.1_Missense_Mutation_p.D1977H|SCN5A_ENST00000425664.1_Missense_Mutation_p.D1960H|SCN5A_ENST00000449557.2_Missense_Mutation_p.D1924H|SCN5A_ENST00000464652.1_5'Flank|SCN5A_ENST00000414099.2_Missense_Mutation_p.D1960H			Q14524	SCN5A_HUMAN	sodium channel, voltage-gated, type V, alpha subunit			107	Medulloblastoma(35;0.163)			Ajmaline(DB01426)|Aprindine(DB01429)|Benzonatate(DB00868)|Carbamazepine(DB00564)|Cinchocaine(DB00527)|Cocaine(DB00907)|Disopyramide(DB00280)|Encainide(DB01228)|Ethotoin(DB00754)|Flecainide(DB01195)|Fosphenytoin(DB01320)|Hexylcaine(DB00473)|Indecainide(DB00192)|Lidocaine(DB00281)|Mexiletine(DB00379)|Moricizine(DB00680)|Oxcarbazepine(DB00776)|Phenytoin(DB00252)|Prilocaine(DB00750)|Procainamide(DB01035)|Propafenone(DB01182)|Quinidine barbiturate(DB01346)|Quinidine(DB00908)|Ranolazine(DB00243)|Riluzole(DB00740)|Tocainide(DB01056)|Valproic Acid(DB00313)|Verapamil(DB00661)|Zonisamide(DB00909)	GTGACACTGTCATAGGAGGGT	0.602000																								0							SO:0001583	missense			ENST00000333535.4	0	1	hg19	CCDS46796.1	.	.	.	.	.	.	.	.	.	.	C	18.180000	3.565807	0.656510	.	.	ENSG00000183873	ENST00000414099;ENST00000423572;ENST00000413689;ENST00000451551;ENST00000443581;ENST00000425664;ENST00000333535;ENST00000455624;ENST00000450102;ENST00000449557	D;D;D;D;D;D;D;D;D;D	0.96856	-4.02;-4.03;-4.03;-4.08;-4.03;-4.02;-4.03;-4.15;-4.08;-4.08	4.950000	4.950000	0.653090	.	0.058474	0.64402	D	0.000003	D	0.95529	0.8547	N	0.08118	0	0.547530	D	0.999986	D;D;P;D;D;D	0.89917	0.959;1.0;0.64;0.999;0.958;1.0	P;D;B;D;P;D	0.85130	0.496;0.997;0.387;0.973;0.693;0.996	D	0.97067	0.9775	10	0.62326	D	0.03	.	18.371400	0.904080	0.0:1.0:0.0:0.0	.	1924;1945;1960;1978;1977;1978	E9PEF3;E9PHB6;E9PG18;Q14524;Q14524-2;E9PEK2	.;.;.;SCN5A_HUMAN;.;.	H	1960;1977;1978;1924;1977;1960;1978;1945;1924;1924	ENSP00000398962:D1960H;ENSP00000398266:D1977H;ENSP00000410257:D1978H;ENSP00000388797:D1924H;ENSP00000397915:D1977H;ENSP00000416634:D1960H;ENSP00000328968:D1978H;ENSP00000399524:D1945H;ENSP00000403355:D1924H;ENSP00000413996:D1924H	ENSP00000328968:D1978H	D	-	1	0	SCN5A	38566935	1	0.714170	9.930000e-01	0.491080	0.998000	0.957120	4.781000	0.623890	2.573000	0.868260	0.655000	0.942530	GAC		TCGA-IB-7897-01A-21D-2201-08	SCN5A-014	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377958.1	0	0	0	7	308	0	42	0	7.142432e-04	0	2	0	42	2		0	0	0	0	0	2	1	9.783250e-01	7	297	0	42	2		0	0	0	0	42	2	-2.839138	1	1	120936	5	16	1	0	0	0	1.972815	0	0.160000	2	0.144951	0.280000	0.120000	0.520000	0.270000	0.304120	0.280000	0	0.190000	0.400000
RBM6	10180	broad.mit.edu	37	3	50005374	50005374	+	Silent	SNP	A	A	T			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr3:50005374A>T	ENST00000266022.4	+	3	775	c.516A>T	c.(514-516)ccA>ccT	p.P172P	RBM6_ENST00000442092.1_Intron|RBM6_ENST00000539992.1_Intron|RBM6_ENST00000441115.1_Intron|RBM6_ENST00000422955.1_Intron|RBM6_ENST00000443081.1_Silent_p.P40P	NM_005777.2	NP_005768.1	P78332	RBM6_HUMAN	RNA binding motif protein 6			33					ATGCTCCTCCATCTGACTTCA	0.468000																								0							SO:0001819	synonymous_variant			ENST00000266022.4	0	1	hg19	CCDS2809.1																																																																																				TCGA-IB-7897-01A-21D-2201-08	RBM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345528.4	0	0	0	7	441	0	69	0	4.165537e-01	1	81	0	69	2		0	0	0	0	0	2	1	9.793298e-01	7	432	0	69	2		0	0	0	0	69	2	-6.820942	1	1	0	0		1	0	0	0	1.972815	0	0.160000	2	0.144951	0.200000	0.080000	0.370000	0.190000	0.215443	0.200000	0	0.130000	0.290000
FGB	2244	broad.mit.edu	37	4	155487741	155487741	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr4:155487741C>A	ENST00000302068.4	+	3	470	c.407C>A	c.(406-408)gCt>gAt	p.A136D	FGB_ENST00000509493.1_Intron|FGB_ENST00000502545.1_3'UTR	NM_005141.4	NP_005132.2	P02675	FIBB_HUMAN	fibrinogen beta chain			34	all_hematologic(180;0.215)	Renal(120;0.0458)		Sucralfate(DB00364)	AATGTGGAAGCTGTTTCCCAG	0.433000													NSCLC(106;1133 1613 21870 46110 52656)											0							SO:0001583	missense			ENST00000302068.4	0	1	hg19	CCDS3786.1	.	.	.	.	.	.	.	.	.	.	C	0.023000	-1.403604	0.011650	.	.	ENSG00000171564	ENST00000302068;ENST00000537843	T	0.80738	-1.41	5.140000	0.887000	0.192000	Fibrinogen, alpha/beta/gamma chain, coiled coil domain (2);	1.797860	0.02358	N	0.076577	T	0.57799	0.2078	N	0.02539	-0.55	0.093100	N	1.000000	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.53739	-0.8396	10	0.07325	T	0.83	.	9.219800	0.373700	0.4197:0.5032:0.0:0.0771	.	119;136	B4E1D3;P02675	.;FIBB_HUMAN	D	136;119	ENSP00000306099:A136D	ENSP00000306099:A136D	A	+	2	0	FGB	155707191	0	0.058580	0	0.037020	0.001000	0.015030	-0.058000	0.117500	-0.020000	0.140320	-1.151000	0.018290	GCT		TCGA-IB-7897-01A-21D-2201-08	FGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317595.1	0	0	0	9	594	0	100	0	8.882272e-04	0	3	0	100	2		0	0	0	0	0	2	1	9.937705e-01	9	583	0	100	2		0	0	0	0	100	2	-7.112338	1	1	0	0		1	1	2	3	2.012271	0	0.160000	2	0.166005	0.200000	0.090000	1.000000	0.190000	0.264082	0.200000	0	0.140000	0.300000
HERC6	55008	broad.mit.edu	37	4	89349856	89349856	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr4:89349856G>A	ENST00000264346.7	+	16	2119	c.2060G>A	c.(2059-2061)cGt>cAt	p.R687H	HERC6_ENST00000380265.5_Missense_Mutation_p.R651H	NM_017912.3	NP_060382.3	Q8IVU3	HERC6_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 6			11		Hepatocellular(203;0.114)			GATGCTCTGCGTCAATTAAGT	0.388000																								0							SO:0001583	missense			ENST00000264346.7	0	1	hg19	CCDS47098.1	.	.	.	.	.	.	.	.	.	.	G	10.400000	1.340412	0.243390	.	.	ENSG00000138642	ENST00000380265;ENST00000264346	T;T	0.77877	0.88;-1.13	4.250000	4.250000	0.503520	HECT (1);	0.116551	0.34002	N	0.004344	T	0.63129	0.2485	L	0.41710	1.295	0.807220	D	1.000000	B;B	0.31817	0.341;0.231	B;B	0.19148	0.024;0.01	T	0.60078	-0.7333	10	0.10902	T	0.67	.	12.355900	0.551760	0.0:0.0:1.0:0.0	.	651;687	Q8IVU3-2;Q8IVU3	.;HERC6_HUMAN	H	651;687	ENSP00000369617:R651H;ENSP00000264346:R687H	ENSP00000264346:R687H	R	+	2	0	HERC6	89568879	4.600000e-02	0.202720	9.970000e-01	0.539660	0.863000	0.493680	0.184000	0.169390	2.356000	0.799430	0.467000	0.429560	CGT		TCGA-IB-7897-01A-21D-2201-08	HERC6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363259.2	0	0	0	3	62	0	16	1	7.034706e-01	4	44	0	16	2		0	0	0	0	0	2	1	8.025600e-01	3	60	0	16	2		0	0	0	0	16	2	-6.781291	1	1	120674	5	36	1	1	2	3	2.012271	0	0.160000	2	0.166005	0.670000	0.190000	1.000000	1.000000	0.678524	0.670000	0	0.380000	1.000000
NIPBL	25836	broad.mit.edu	37	5	37044451	37044451	+	Silent	SNP	G	G	T			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr5:37044451G>T	ENST00000282516.8	+	35	6610	c.6111G>T	c.(6109-6111)acG>acT	p.T2037T	NIPBL_ENST00000448238.2_Silent_p.T2037T	NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	Q6KC79	NIPBL_HUMAN	Nipped-B homolog (Drosophila)			128	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)		TCTTATAGACGCAAAATGATT	0.358000																								0							SO:0001819	synonymous_variant			ENST00000282516.8	0	1	hg19	CCDS3920.1																																																																																				TCGA-IB-7897-01A-21D-2201-08	NIPBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207582.1	0	0	0	4	175	0	24	0	5.566914e-01	0	73	0	24	2		0	0	0	0	0	2	1	8.886388e-01	5	172	0	24	2		0	0	0	0	24	2	-3.275064	1	1	0	0		1	1	2	3	2.010679	0	0.160000	2	0.165342	0.320000	0.100000	1.000000	0.280000	0.380321	0.320000	0	0.190000	0.530000
VARS2	57176	broad.mit.edu	37	6	30892256	30892256	+	Silent	SNP	C	C	G			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr6:30892256C>G	ENST00000321897.5	+	25	3224	c.2592C>G	c.(2590-2592)ctC>ctG	p.L864L	VARS2_ENST00000416670.2_Silent_p.L864L|VARS2_ENST00000476162.1_3'UTR|VARS2_ENST00000542001.1_Silent_p.L724L|VARS2_ENST00000541562.1_Silent_p.L894L			Q5ST30	SYVM_HUMAN	valyl-tRNA synthetase 2, mitochondrial			46					CTGAAGAGCTCTGGCAGAGGC	0.706000																								0							SO:0001819	synonymous_variant			ENST00000321897.5	1	1	hg19	CCDS34387.1																																																																																				TCGA-IB-7897-01A-21D-2201-08	VARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076566.2	0	0	0	7	334	0	48	0	2.354994e-02	0	10	0	48	2		0	0	0	0	0	2	1	9.752468e-01	5	312	0	48	2		0	0	0	0	48	2	-7.410055	1	1	0	0		1	0	0	0	1.978661	0	0.160000	2	0.147727	0.260000	0.110000	0.490000	0.250000	0.282500	0.260000	0	0.180000	0.370000
HLA-DMA	3108	broad.mit.edu	37	6	32917503	32917503	+	Silent	SNP	G	G	A			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr6:32917503G>A	ENST00000374843.4	-	3	622	c.537C>T	c.(535-537)gtC>gtT	p.V179V	HLA-DMA_ENST00000395305.3_Silent_p.V84V|XXbac-BPG181M17.5_ENST00000429234.1_Intron|HLA-DMA_ENST00000395303.3_Silent_p.V145V|HLA-DMA_ENST00000464392.1_5'UTR	NM_006120.3	NP_006111.2	P28067	DMA_HUMAN	major histocompatibility complex, class II, DM alpha			11					TGAGTCCATCGACAGCTGAGA	0.473000																								0							SO:0001819	synonymous_variant			ENST00000374843.4	0	1	hg19	CCDS4761.1																																																																																				TCGA-IB-7897-01A-21D-2201-08	HLA-DMA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076325.2	0	0	0	7	388	0	65	1	9.967484e-01	14	595	0	65	2		0	0	0	0	0	2	1	9.795516e-01	6	382	0	65	2		0	0	0	0	65	2	-6.572624	1	0	0	0		1	0	1	1	1.971995	0	0.160000	2	0.147727	0.220000	0.100000	0.420000	0.220000	0.244645	0.220000	0	0.150000	0.320000
DAAM2	23500	broad.mit.edu	37	6	39847105	39847105	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr6:39847105C>T	ENST00000398904.2	+	14	1879	c.1697C>T	c.(1696-1698)cCg>cTg	p.P566L	DAAM2_ENST00000274867.4_Missense_Mutation_p.P566L|RP11-61I13.3_ENST00000607675.1_RNA|DAAM2_ENST00000538976.1_Missense_Mutation_p.P566L			Q86T65	DAAM2_HUMAN	dishevelled associated activator of morphogenesis 2			49	Ovarian(28;0.0355)|Colorectal(47;0.196)				GGGGGACCCCCGACTCCCCCA	0.672000																								0							SO:0001583	missense			ENST00000398904.2	0	1	hg19	CCDS56426.1	.	.	.	.	.	.	.	.	.	.	C	12.370000	1.918426	0.339080	.	.	ENSG00000146122	ENST00000274867;ENST00000398904;ENST00000538976	D;D;D	0.92446	-3.04;-3.04;-3.04	4.630000	4.630000	0.577260	Actin-binding FH2 (1);	0.000000	0.85682	D	0.000000	D	0.90143	0.6920	L	0.47716	1.5	0.807220	D	1.000000	D;D	0.61080	0.989;0.982	P;P	0.51170	0.661;0.459	D	0.89794	0.3970	10	0.42905	T	0.14	.	17.262900	0.870750	0.0:1.0:0.0:0.0	.	566;566	G5EA45;Q86T65	.;DAAM2_HUMAN	L	566	ENSP00000274867:P566L;ENSP00000381876:P566L;ENSP00000437808:P566L	ENSP00000274867:P566L	P	+	2	0	DAAM2	39955083	9.990000e-01	0.422020	9.780000e-01	0.431390	0.008000	0.064300	4.374000	0.595430	2.383000	0.812150	0.650000	0.862430	CCG		TCGA-IB-7897-01A-21D-2201-08	DAAM2-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280648.1	0	0	0	4	138	0	33	0	3.325286e-02	0	8	0	33	2		0	0	0	0	0	2	1	8.773031e-01	4	130	0	31	2		0	0	0	0	33	2	-6.605908	1	1	0	0		1	1	2	3	2.011705	0	0.160000	2	0.166005	0.400000	0.130000	1.000000	0.340000	0.463179	0.400000	0	0.240000	0.680000
FOXP2	93986	broad.mit.edu	37	7	114298280	114298280	+	Nonsense_Mutation	SNP	C	C	T			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr7:114298280C>T	ENST00000393494.2	+	11	1705	c.1426C>T	c.(1426-1428)Cga>Tga	p.R476*	FOXP2_ENST00000393500.3_3'UTR|FOXP2_ENST00000393498.2_Nonsense_Mutation_p.R455*|FOXP2_ENST00000350908.4_Nonsense_Mutation_p.R476*|FOXP2_ENST00000393491.3_Intron|FOXP2_ENST00000403559.4_Nonsense_Mutation_p.R493*|FOXP2_ENST00000408937.3_Nonsense_Mutation_p.R501*|FOXP2_ENST00000393489.3_Nonsense_Mutation_p.R384*			O15409	FOXP2_HUMAN	forkhead box P2			52					GGGAGCCATACGAAGGCGACA	0.507000																								0							SO:0001587	stop_gained			ENST00000393494.2	0	1	hg19	CCDS5760.1	.	.	.	.	.	.	.	.	.	.	C	39.000000	7.583133	0.983710	.	.	ENSG00000128573	ENST00000393494;ENST00000408937;ENST00000403559;ENST00000350908;ENST00000393498;ENST00000393489	.	.	.	5.710000	5.710000	0.891250	.	0.113270	0.64402	D	0.000007	.	.	.	.	.	.	0.807220	D	1.000000	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	20.224500	0.983370	0.0:1.0:0.0:0.0	.	.	.	.	X	476;501;493;476;453;384	.	ENSP00000265436:R476X	R	+	1	2	FOXP2	114085516	1	0.714170	1	0.803570	0.999000	0.989320	3.664000	0.545250	2.861000	0.982270	0.650000	0.862430	CGA		TCGA-IB-7897-01A-21D-2201-08	FOXP2-014	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317366.1	0	0	0	15	444	0	74	0	1.187377e-01	0	17	0	74	2		0	0	0	0	0	2	1	9.998203e-01	15	422	0	73	2		0	0	0	0	74	2	-13.937700	1	1	0	0		1	1	2	3	2.011317	0	0.160000	2	0.165342	0.420000	0.240000	1.000000	0.410000	0.468378	0.420000	0	0.320000	0.570000
LRP12	29967	broad.mit.edu	37	8	105502937	105502937	+	Silent	SNP	G	G	A			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr8:105502937G>A	ENST00000276654.5	-	7	2652	c.2544C>T	c.(2542-2544)aaC>aaT	p.N848N	LRP12_ENST00000424843.2_Silent_p.N829N|LRP12_ENST00000518375.1_5'UTR	NM_013437.4	NP_038465.1	Q9Y561	LRP12_HUMAN	low density lipoprotein receptor-related protein 12			48			OV - Ovarian serous cystadenocarcinoma(57;1.21e-06)|STAD - Stomach adenocarcinoma(118;0.229)		CACTCGTTTCGTTTTTCAGTG	0.418000																								0							SO:0001819	synonymous_variant			ENST00000276654.5	0	1	hg19	CCDS6303.1																																																																																				TCGA-IB-7897-01A-21D-2201-08	LRP12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380821.1	0	0	0	13	622	0	81	0	4.874092e-01	1	75	0	81	2		0	0	0	0	0	2	1	9.994466e-01	13	606	0	81	2		0	0	0	0	81	2	-2.786688	1	1	121410	8	41	1	1	2	3	2.011482	0	0.160000	2	0.165342	0.260000	0.140000	1.000000	0.260000	0.320979	0.260000	0	0.200000	0.370000
PLEC	5339	broad.mit.edu	37	8	145006714	145006714	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr8:145006714G>A	ENST00000322810.4	-	16	2411	c.2242C>T	c.(2242-2244)Cgc>Tgc	p.R748C	PLEC_ENST00000436759.2_Missense_Mutation_p.R638C|PLEC_ENST00000354589.3_Missense_Mutation_p.R611C|PLEC_ENST00000527096.1_Missense_Mutation_p.R634C|PLEC_ENST00000357649.2_Missense_Mutation_p.R615C|PLEC_ENST00000354958.2_Missense_Mutation_p.R589C|PLEC_ENST00000345136.3_Missense_Mutation_p.R611C|PLEC_ENST00000356346.3_Missense_Mutation_p.R597C|PLEC_ENST00000398774.2_Missense_Mutation_p.R579C	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	p.R611C(1)|p.R748C(1)|p.R638C(1)		137					GACCTGAGGCGGGCCTTGGAG	0.657000																								3	Substitution - Missense(3)						SO:0001583	missense			ENST00000322810.4	0	1	hg19	CCDS43772.1	.	.	.	.	.	.	.	.	.	.	G	12.410000	1.930956	0.340960	.	.	ENSG00000178209	ENST00000345136;ENST00000357649;ENST00000354589;ENST00000398774;ENST00000322810;ENST00000354958;ENST00000356346;ENST00000436759;ENST00000527096;ENST00000528025	T;T;T;T;T;T;T;T;T;D	0.96334	-0.02;-0.02;-0.02;-0.02;-0.02;-0.02;-0.02;-0.02;-0.02;-3.98	4.600000	3.710000	0.425840	.	0.000000	0.64402	U	0.000005	D	0.97838	0.9290	M	0.84773	2.715	0.807220	D	1.000000	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.85130	0.997;0.997;0.997;0.994;0.997;0.997;0.997;0.997	D	0.97902	1.0303	10	0.87932	D	0	.	11.350300	0.495830	0.0925:0.0:0.9075:0.0	.	638;597;589;748;579;611;615;611	Q15149-2;Q15149-9;Q15149-8;Q15149;Q15149-7;Q15149-5;Q15149-6;Q15149-4	.;.;.;PLEC_HUMAN;.;.;.;.	C	611;615;611;579;748;589;597;638;634;655	ENSP00000344848:R611C;ENSP00000350277:R615C;ENSP00000346602:R611C;ENSP00000381756:R579C;ENSP00000323856:R748C;ENSP00000347044:R589C;ENSP00000348702:R597C;ENSP00000388180:R638C;ENSP00000434583:R634C;ENSP00000437303:R655C	ENSP00000323856:R748C	R	-	1	0	PLEC	145078702	1	0.714170	1	0.803570	0.558000	0.355540	6.203000	0.721370	2.271000	0.756650	0.453000	0.300090	CGC		TCGA-IB-7897-01A-21D-2201-08	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	0	0	0	11	648	0	110	1	7.092220e-01	13	132	0	110	2		0	0	0	0	0	2	1	9.979377e-01	11	623	0	106	2		0	0	0	0	110	2	-2.968742	1	1	120706	2	33	1	1	2	3	2.011482	0	0.160000	2	0.165342	0.220000	0.110000	1.000000	0.210000	0.276392	0.220000	0	0.150000	0.310000
PTGS1	5742	broad.mit.edu	37	9	125148756	125148756	+	Silent	SNP	C	C	T			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr9:125148756C>T	ENST00000362012.2	+	9	1046	c.1041C>T	c.(1039-1041)taC>taT	p.Y347Y	PTGS1_ENST00000223423.4_Silent_p.Y347Y|PTGS1_ENST00000540753.1_Silent_p.Y322Y|PTGS1_ENST00000373698.5_Silent_p.Y238Y|AL162424.1_ENST00000600713.1_Intron	NM_000962.3|NM_001271164.1|NM_001271367.1|NM_080591.2	NP_000953.2|NP_001258093.1|NP_001258296.1|NP_542158.1	P23219	PGH1_HUMAN	prostaglandin-endoperoxide synthase 1 (prostaglandin G/H synthase and cyclooxygenase)			8				Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Antipyrine(DB01435)|Antrafenine(DB01419)|Balsalazide(DB01014)|Bortezomib(DB00188)|Bromfenac(DB00963)|Candesartan(DB00796)|Carprofen(DB00821)|Carvedilol(DB01136)|Chlorpropamide(DB00672)|Dapsone(DB00250)|Desmopressin(DB00035)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylcarbamazine(DB00711)|Diflunisal(DB00861)|Dihomo-gamma-linolenic acid(DB00154)|Diphenhydramine(DB01075)|Dronabinol(DB00470)|Eletriptan(DB00216)|Eszopiclone(DB00402)|Etodolac(DB00749)|Etoposide(DB00773)|Fenoprofen(DB00573)|Flurbiprofen(DB00712)|Hexobarbital(DB01355)|Hydromorphone(DB00327)|Ibuprofen(DB01050)|Icosapent(DB00159)|Ifosfamide(DB01181)|Imatinib(DB00619)|Indomethacin(DB00328)|Irbesartan(DB01029)|Ketamine(DB01221)|Ketobemidone(DB06738)|Ketoprofen(DB01009)|Ketorolac(DB00465)|Lornoxicam(DB06725)|Lumiracoxib(DB01283)|Magnesium salicylate(DB01397)|Meclofenamic acid(DB00939)|Mefenamic acid(DB00784)|Meloxicam(DB00814)|Mesalazine(DB00244)|Minoxidil(DB00350)|Montelukast(DB00471)|Nabumetone(DB00461)|Naproxen(DB00788)|Nateglinide(DB00731)|Nepafenac(DB06802)|Niflumic Acid(DB04552)|Nortriptyline(DB00540)|Oxaprozin(DB00991)|Phenylbutazone(DB00812)|Pioglitazone(DB01132)|Piroxicam(DB00554)|Rosiglitazone(DB00412)|Salicylate-sodium(DB01398)|Salicylic acid(DB00936)|Salsalate(DB01399)|Sulfamethoxazole(DB01015)|Sulfasalazine(DB00795)|Sulindac(DB00605)|Suprofen(DB00870)|Tenoxicam(DB00469)|Terbinafine(DB00857)|Thalidomide(DB01041)|Tiaprofenic acid(DB01600)|Tolmetin(DB00500)|Torasemide(DB00214)|Trabectedin(DB05109)|Triflusal(DB08814)|Trisalicylate-choline(DB01401)|Valproic Acid(DB00313)|Voriconazole(DB00582)|Zafirlukast(DB00549)|Zileuton(DB00744)|Zolpidem(DB00425)|Zopiclone(DB01198)	TCGAGGAGTACGTGCAGCAGC	0.527000																								0							SO:0001819	synonymous_variant			ENST00000362012.2	1	1	hg19	CCDS6842.1																																																																																				TCGA-IB-7897-01A-21D-2201-08	PTGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053933.1	0	0	0	22	1054	0	137	1	2.107155e-01	2	38	0	137	2		0	0	0	0	0	2	1	9.999983e-01	22	1035	0	136	2		0	0	0	0	137	2	-2.856811	1	1	121412	2	39	1	0	0	0	1.960649	0	0.160000	2	0.139344	0.240000	0.150000	0.360000	0.250000	0.258803	0.240000	0	0.200000	0.310000
ROR2	4920	broad.mit.edu	37	9	94486741	94486741	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr9:94486741C>T	ENST00000375708.3	-	9	2233	c.2035G>A	c.(2035-2037)Ggt>Agt	p.G679S	ROR2_ENST00000550066.1_5'UTR|ROR2_ENST00000375715.1_Missense_Mutation_p.G539S	NM_004560.3	NP_004551.2	Q01974	ROR2_HUMAN	receptor tyrosine kinase-like orphan receptor 2			71					AGGACCACACCGTAGGACCAG	0.607000																								0							SO:0001583	missense			ENST00000375708.3	0	1	hg19	CCDS6691.1	.	.	.	.	.	.	.	.	.	.	C	17.590000	3.427881	0.627330	.	.	ENSG00000169071	ENST00000375715;ENST00000375708	D;D	0.99150	-5.49;-5.49	4.860000	4.860000	0.630820	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.42420	D	0.000712	D	0.99471	0.9812	M	0.93638	3.44	0.807220	D	1.000000	D;D	0.76494	0.995;0.999	P;D	0.75020	0.797;0.985	D	0.98372	1.0554	10	0.87932	D	0	.	18.208700	0.898630	0.0:1.0:0.0:0.0	.	679;539	Q01974;B1APY4	ROR2_HUMAN;.	S	539;679	ENSP00000364867:G539S;ENSP00000364860:G679S	ENSP00000364860:G679S	G	-	1	0	ROR2	93526562	1	0.714170	1	0.803570	0.446000	0.321370	5.842000	0.694170	2.526000	0.851670	0.561000	0.740990	GGT		TCGA-IB-7897-01A-21D-2201-08	ROR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053040.1	0	0	0	6	244	0	47	0	2.740425e-01	0	37	0	47	2		0	0	0	0	0	2	1	9.613594e-01	5	236	0	44	2		0	0	0	0	47	2	-7.143834	1	1	0	0		1	0	0	0	1.962861	0	0.160000	2	0.140753	0.310000	0.120000	0.590000	0.280000	0.331185	0.310000	0	0.200000	0.450000
MAGEA3	4102	broad.mit.edu	37	X	151935609	151935609	+	Silent	SNP	G	G	A			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chrX:151935609G>A	ENST00000393902.3	-	3	1125	c.558C>T	c.(556-558)taC>taT	p.Y186Y	MAGEA3_ENST00000370278.3_Silent_p.Y186Y			P43357	MAGA3_HUMAN	melanoma antigen family A, 3			15	Acute lymphoblastic leukemia(192;6.56e-05)				GCAGGCCATCGTAGGAGAGGC	0.572000																								0							SO:0001819	synonymous_variant			ENST00000393902.3	1	1	hg19	CCDS14715.1																																																																																				TCGA-IB-7897-01A-21D-2201-08	MAGEA3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058744.1	0	0	0	27	1152	0	223		0	0	0	0	223	2		0	0	0	0	0	2	1	9.999999e-01	27	1125	0	223	2		0	0	0	0	223	2	-2.813178	1	1	121180	12	43	1	0	1	1			0.160000	2	0.160000	0.280000	0.190000	0.400000	0.280000	0.295026	0.280000	0	0.230000	0.350000
