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
CTSB	1508	broad.mit.edu	37	8	11705590	11705591	+	Frame_Shift_Ins	INS	-	-	A			TCGA-IB-7887-01A-11D-2154-08	TCGA-IB-7887-10A-01D-2154-08			-	A	-	-		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	35c4c115-e867-4ae4-987f-9ff02003be62	73139364-4a90-4b65-82fb-efa77a95b3fa	g.chr8:11705590_11705591insA	ENST00000353047.6	-	6	770_771	c.517_518insT	c.(517-519)tatfs	p.Y173fs	CTSB_ENST00000534510.1_Frame_Shift_Ins_p.Y173fs|CTSB_ENST00000453527.2_Frame_Shift_Ins_p.Y173fs|CTSB_ENST00000533455.1_Frame_Shift_Ins_p.Y173fs|CTSB_ENST00000530640.2_Frame_Shift_Ins_p.Y173fs|CTSB_ENST00000415599.2_3'UTR|RP11-589N15.2_ENST00000602711.1_RNA|CTSB_ENST00000525076.1_5'Flank|CTSB_ENST00000531089.1_Frame_Shift_Ins_p.Y173fs|CTSB_ENST00000345125.3_Frame_Shift_Ins_p.Y173fs|CTSB_ENST00000434271.1_Frame_Shift_Ins_p.Y173fs	NM_001908.3	NP_001899.1	P07858	CATB_HUMAN	cathepsin B			16	all_epithelial(15;0.205)		STAD - Stomach adenocarcinoma(15;0.00546)		ATGGGATTCATAGAGGCCACCA	0.450000																								0							SO:0001589	frameshift_variant			ENST00000353047.6	0	1	hg19	CCDS5986.1																																																																																				TCGA-IB-7887-01A-11D-2154-08	CTSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207586.3	1	0	0	62	503	0	111	0	1	1	1387	0	111	2	0	0	0	0	0	0		1	1.000000	63	499	0	111	2	0	0	0	0	0	0		-19.974620	1	1	0	0		1	0	1	1	1.802685	1	0.270000	1.780000	0.156069	0.690000	0.540000	0.860000	0.700000	0.704933	0.690000	0	6.100000e-01	7.800000e-01
DCHS1	8642	broad.mit.edu	37	11	6662161	6662161	+	Nonsense_Mutation	SNP	A	A	C			TCGA-IB-7887-01A-11D-2154-08	TCGA-IB-7887-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35c4c115-e867-4ae4-987f-9ff02003be62	73139364-4a90-4b65-82fb-efa77a95b3fa	g.chr11:6662161A>C	ENST00000299441.3	-	2	1095	c.684T>G	c.(682-684)taT>taG	p.Y228*		NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1			103		Medulloblastoma(188;0.00263)|all_neural(188;0.026)			AACCACCATCATAGGCCTCCA	0.602000																								0							SO:0001587	stop_gained			ENST00000299441.3	0	1	hg19	CCDS7771.1	.	.	.	.	.	.	.	.	.	.	A	37	6.418677	0.97550	.	.	ENSG00000166341	ENST00000299441	.	.	.	4.18	-1.56	0.08532	.	0.000000	0.42294	D	0.000731	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.368	0.44035	0.6186:0.0:0.3814:0.0	.	.	.	.	X	228	.	ENSP00000299441:Y228X	Y	-	3	2	DCHS1	6618737	0.966000	0.33281	0.995000	0.50966	0.991000	0.79684	0.258000	0.18387	-0.379000	0.07906	0.445000	0.29226	TAT		TCGA-IB-7887-01A-11D-2154-08	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	1	0	1	111	559	0	114	0	5.675710e-01	0	11	0	114	2		0	0	0	0	0	2	1	1.000000	109	552	0	114	2		0	0	0	0	114	2	-20.000000	1	1	0	0		1	0	1	1	1.779903	1	0.270000	1.780000	0.156069	0.950000	0.840000	1.000000	0.990000	0.950780	0.950000	1	9.000000e-01	9.900000e-01
KRAS	3845	broad.mit.edu	37	12	25398285	25398285	+	Missense_Mutation	SNP	C	C	G	rs121913530		TCGA-IB-7887-01A-11D-2154-08	TCGA-IB-7887-10A-01D-2154-08			C	G	C	C		Valid	Somatic	Phase_I	WXS	KRAS_deep			Illumina GAIIx	35c4c115-e867-4ae4-987f-9ff02003be62	73139364-4a90-4b65-82fb-efa77a95b3fa	g.chr12:25398285C>G	ENST00000256078.4	-	2	97	c.34G>C	c.(34-36)Ggt>Cgt	p.G12R	KRAS_ENST00000556131.1_Missense_Mutation_p.G12R|KRAS_ENST00000557334.1_Missense_Mutation_p.G12R|KRAS_ENST00000311936.3_Missense_Mutation_p.G12R	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	p.G12C(3001)|p.G12S(1288)|p.G12R(789)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12W(3)|p.A11_G12insGA(2)|p.G12Y(2)|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)		CCTACGCCACCAGCTCCAACT	0.348000	G12C(CALU1_LUNG)|G12C(HCC44_LUNG)|G12C(IALM_LUNG)|G12C(KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12C(KYSE410_OESOPHAGUS)|G12C(LU65_LUNG)|G12C(LU99_LUNG)|G12C(MIAPACA2_PANCREAS)|G12C(NCIH1373_LUNG)|G12C(NCIH1792_LUNG)|G12C(NCIH2030_LUNG)|G12C(NCIH2122_LUNG)|G12C(NCIH23_LUNG)|G12C(NCIH358_LUNG)|G12C(OV56_OVARY)|G12C(SW1463_LARGE_INTESTINE)|G12C(SW1573_LUNG)|G12C(SW837_LARGE_INTESTINE)|G12C(UMUC3_URINARY_TRACT)|G12R(CAL62_THYROID)|G12R(HS274T_BREAST)|G12R(HUPT3_PANCREAS)|G12R(KP2_PANCREAS)|G12R(PSN1_PANCREAS)|G12R(TCCPAN2_PANCREAS)|G12S(A549_LUNG)|G12S(KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12S(LS123_LARGE_INTESTINE)	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	5144	Substitution - Missense(5142)|Insertion - In frame(2)	GRCh37	CM076251	KRAS	M	rs121913530	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	0	1	hg19	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	28.6	4.930538	0.92389	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78246	-1.16;-1.16;-1.16;-1.16	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.84893	0.5573	M	0.84082	2.675	0.80722	D	1	P;P	0.43287	0.802;0.741	B;P	0.47941	0.36;0.562	D	0.86658	0.1902	10	0.66056	D	0.02	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	R	12	ENSP00000308495:G12R;ENSP00000452512:G12R;ENSP00000256078:G12R;ENSP00000451856:G12R	ENSP00000256078:G12R	G	-	1	0	KRAS	25289552	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT		TCGA-IB-7887-01A-11D-2154-08	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	1	0	0	20	132	1	23	1	1.691198e-01	9	18	1	23	6	1	1	62	365	0	447	2	1	0.659073	20	128	1	23	18	1	9.910251e-01	653	7363	1	23	627	-11.314890	1	1	0	0		1	2	2	4	2.192614	1	0.270000	1.780000	0.314425	0.990000	0.680000	1.000000	1.000000	0.952741	0.990000	1	8.600000e-01	1
FOXJ2	55810	broad.mit.edu	37	12	8205432	8205432	+	Missense_Mutation	SNP	G	G	C			TCGA-IB-7887-01A-11D-2154-08	TCGA-IB-7887-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35c4c115-e867-4ae4-987f-9ff02003be62	73139364-4a90-4b65-82fb-efa77a95b3fa	g.chr12:8205432G>C	ENST00000162391.3	+	11	2856	c.1711G>C	c.(1711-1713)Gac>Cac	p.D571H	FOXJ2_ENST00000539192.1_3'UTR	NM_018416.2	NP_060886.1	Q9P0K8	FOXJ2_HUMAN	forkhead box J2			16					CTTCGACTGGGACTTGATCAC	0.552000																								0							SO:0001583	missense			ENST00000162391.3	0	1	hg19	CCDS8587.1	.	.	.	.	.	.	.	.	.	.	G	25.4	4.637902	0.87760	.	.	ENSG00000065970	ENST00000162391	D	0.99311	-5.73	5.85	5.85	0.93711	.	0.244803	0.28724	N	0.014344	D	0.99254	0.9740	M	0.63843	1.955	0.80722	D	1	D	0.76494	0.999	D	0.81914	0.995	D	0.99819	1.1046	10	0.87932	D	0	.	17.6544	0.88174	0.0:0.0:1.0:0.0	.	571	Q9P0K8	FOXJ2_HUMAN	H	571	ENSP00000162391:D571H	ENSP00000162391:D571H	D	+	1	0	FOXJ2	8096699	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	6.918000	0.75788	2.772000	0.95346	0.650000	0.86243	GAC		TCGA-IB-7887-01A-11D-2154-08	FOXJ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400088.1	1	0	0	6	107	0	20	1	4.390966e-01	7	18	0	20	2		0	0	0	0	0	2	1	0.957759	6	99	0	20	2		0	0	0	0	20	2	-9.940343	1	1	0	0		1	2	2	4	2.194364	1	0.270000	1.780000	0.316159	0.490000	0.190000	1.000000	0.410000	0.566397	0.490000	0	3.100000e-01	1
SACS	26278	broad.mit.edu	37	13	23906194	23906194	+	Nonsense_Mutation	SNP	G	G	A			TCGA-IB-7887-01A-11D-2154-08	TCGA-IB-7887-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35c4c115-e867-4ae4-987f-9ff02003be62	73139364-4a90-4b65-82fb-efa77a95b3fa	g.chr13:23906194G>A	ENST00000382292.3	-	9	12094	c.11821C>T	c.(11821-11823)Caa>Taa	p.Q3941*	SACS_ENST00000402364.1_Nonsense_Mutation_p.Q3191*|SACS_ENST00000382298.3_Nonsense_Mutation_p.Q3941*			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone			189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)			ACTAACATTTGCACACCAATA	0.403000																								0							SO:0001587	stop_gained			ENST00000382292.3	0	1	hg19	CCDS9300.2	.	.	.	.	.	.	.	.	.	.	G	58	33.524865	0.99981	.	.	ENSG00000151835	ENST00000382292;ENST00000402364;ENST00000382298	.	.	.	5.82	5.82	0.92795	.	0.053109	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.39692	T	0.17	.	20.1013	0.97878	0.0:0.0:1.0:0.0	.	.	.	.	X	3941;3191;3941	.	ENSP00000371729:Q3941X	Q	-	1	0	SACS	22804194	1.000000	0.71417	0.990000	0.47175	0.948000	0.59901	9.865000	0.99609	2.748000	0.94277	0.655000	0.94253	CAA		TCGA-IB-7887-01A-11D-2154-08	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	1	0	0	85	683	0	102	1	5.443034e-01	2	14	0	102	2		0	0	0	0	0	2	1	1.000000	85	669	0	102	2		0	0	0	0	102	2	-20.000000	1	1	0	0		1	1	2	3	2.062589	0	0.270000	1.780000	0.270984	0.810000	0.660000	1.000000	0.820000	0.824706	0.810000	0	7.300000e-01	9.100000e-01
POTEG	404785	broad.mit.edu	37	14	19553582	19553582	+	Missense_Mutation	SNP	A	A	T			TCGA-IB-7887-01A-11D-2154-08	TCGA-IB-7887-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35c4c115-e867-4ae4-987f-9ff02003be62	73139364-4a90-4b65-82fb-efa77a95b3fa	g.chr14:19553582A>T	ENST00000409832.3	+	1	218	c.166A>T	c.(166-168)Aca>Tca	p.T56S		NM_001005356.2	NP_001005356.1	Q6S5H5	POTEG_HUMAN	POTE ankyrin domain family, member G			47					TGCTATGAAGACACTCAGGAG	0.617000																								0							SO:0001583	missense			ENST00000409832.3	1	1	hg19	CCDS32018.1	.	.	.	.	.	.	.	.	.	.	a	10.49	1.364135	0.24684	.	.	ENSG00000222036	ENST00000409832	T	0.29397	1.57	.	.	.	.	.	.	.	.	T	0.23727	0.0574	L	0.43152	1.355	0.09310	N	1	P	0.35745	0.518	B	0.36418	0.224	T	0.17745	-1.0359	7	0.56958	D	0.05	.	.	.	.	.	56	Q6S5H5	POTEG_HUMAN	S	56	ENSP00000386971:T56S	ENSP00000386971:T56S	T	+	1	0	POTEG	18623582	0.003000	0.15002	0.006000	0.13384	0.006000	0.05464	0.468000	0.22051	0.141000	0.18875	0.139000	0.15985	ACA		TCGA-IB-7887-01A-11D-2154-08	POTEG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408579.1	0	0	0	97	3062	0	550		0	0	0	0	550	2		0	0	0	0	0	2	1	1.000000	53	1800	0	808	2		0	0	0	0	550	2	-3.191071	1	1	0	0		1						0.270000	1.780000									0	0
FAM179B	23116	broad.mit.edu	37	14	45473306	45473306	+	Missense_Mutation	SNP	T	T	C			TCGA-IB-7887-01A-11D-2154-08	TCGA-IB-7887-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35c4c115-e867-4ae4-987f-9ff02003be62	73139364-4a90-4b65-82fb-efa77a95b3fa	g.chr14:45473306T>C	ENST00000361577.3	+	4	2595	c.2381T>C	c.(2380-2382)tTt>tCt	p.F794S	FAM179B_ENST00000382233.2_Missense_Mutation_p.F794S|KLHL28_ENST00000553817.1_Intron|FAM179B_ENST00000361462.2_Missense_Mutation_p.F794S	NM_015091.2	NP_055906.2	Q9Y4F4	F179B_HUMAN	family with sequence similarity 179, member B			45					CAGCAAACATTTGGTAGTCAA	0.363000																								0							SO:0001583	missense			ENST00000361577.3	1	1	hg19	CCDS9681.1	.	.	.	.	.	.	.	.	.	.	T	19.28	3.798217	0.70567	.	.	ENSG00000198718	ENST00000429476;ENST00000361577;ENST00000361462;ENST00000382233;ENST00000555874	T;T;T;T	0.13538	2.58;2.58;4.05;4.05	5.56	4.4	0.53042	Armadillo-type fold (1);	0.352636	0.27253	N	0.020216	T	0.17916	0.0430	N	0.24115	0.695	0.27467	N	0.952969	P;D;D	0.62365	0.567;0.974;0.991	B;P;P	0.56563	0.175;0.57;0.801	T	0.02901	-1.1096	10	0.87932	D	0	-10.7199	11.2492	0.49015	0.0:0.0:0.1532:0.8468	.	794;794;794	G3XAE9;Q9Y4F4;Q9Y4F4-2	.;F179B_HUMAN;.	S	794;794;794;794;113	ENSP00000355045:F794S;ENSP00000354917:F794S;ENSP00000371668:F794S;ENSP00000451141:F113S	ENSP00000354917:F794S	F	+	2	0	FAM179B	44543056	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.528000	0.53524	0.916000	0.36871	0.460000	0.39030	TTT		TCGA-IB-7887-01A-11D-2154-08	FAM179B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276791.1	1	0	1	51	260	0	27	1	8.931436e-01	8	14	0	27	2		0	0	0	0	0	2	1	1.000000	51	254	0	26	2		0	0	0	0	27	2	-20.000000	1	1	0	0		1	0	1	1	2.054966	0	0.270000	1.780000	0.268024	0.990000	0.920000	1.000000	1.000000	0.995573	0.990000	1	9.900000e-01	1
VAC14	55697	broad.mit.edu	37	16	70726807	70726807	+	Silent	SNP	G	G	A			TCGA-IB-7887-01A-11D-2154-08	TCGA-IB-7887-10A-01D-2154-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	35c4c115-e867-4ae4-987f-9ff02003be62	73139364-4a90-4b65-82fb-efa77a95b3fa	g.chr16:70726807G>A	ENST00000261776.5	-	18	2363	c.2103C>T	c.(2101-2103)ctC>ctT	p.L701L	VAC14_ENST00000571759.1_5'Flank|VAC14_ENST00000536184.2_Silent_p.L133L	NM_018052.3	NP_060522.3	Q08AM6	VAC14_HUMAN	Vac14 homolog (S. cerevisiae)			33		Ovarian(137;0.0699)			GCAGGAGCATGAGCAGGCCGT	0.662000																								0							SO:0001819	synonymous_variant			ENST00000261776.5	0	1	hg19	CCDS10896.1																																																																																				TCGA-IB-7887-01A-11D-2154-08	VAC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268973.3	1	0	1	16	97	0	10	1	9.999064e-01	46	56	0	10	2		0	0	0	0	0	2	1	0.999941	16	93	0	9	2		0	0	0	0	10	2	-20.000000	1	1	120788	3	30	1	0	1	1	2.059000	0	0.270000	1.780000	0.269013	0.990000	0.640000	1.000000	1.000000	0.937106	0.990000	1	8.200000e-01	1
KRT31	3881	broad.mit.edu	37	17	39551782	39551782	+	Missense_Mutation	SNP	T	T	C			TCGA-IB-7887-01A-11D-2154-08	TCGA-IB-7887-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35c4c115-e867-4ae4-987f-9ff02003be62	73139364-4a90-4b65-82fb-efa77a95b3fa	g.chr17:39551782T>C	ENST00000251645.2	-	4	734	c.682A>G	c.(682-684)Acc>Gcc	p.T228A		NM_002277.2	NP_002268.2	Q15323	K1H1_HUMAN	keratin 31			31		Breast(137;0.000496)			TGACTCCTGGTCTCGTTCAGC	0.597000																								0							SO:0001583	missense			ENST00000251645.2	1	1	hg19	CCDS11391.1	.	.	.	.	.	.	.	.	.	.	t	13.06	2.125541	0.37533	.	.	ENSG00000094796	ENST00000251645	D	0.88586	-2.4	5.4	4.33	0.51752	Filament (1);	0.180058	0.39759	N	0.001269	D	0.86764	0.6011	L	0.50333	1.59	0.31092	N	0.710708	B	0.22604	0.072	B	0.32980	0.156	D	0.84831	0.0802	10	0.87932	D	0	.	10.2699	0.43477	0.0:0.0774:0.0:0.9226	.	228	Q15323	K1H1_HUMAN	A	228	ENSP00000251645:T228A	ENSP00000251645:T228A	T	-	1	0	KRT31	36805308	0.978000	0.34361	0.998000	0.56505	0.529000	0.34654	1.848000	0.39309	0.888000	0.36160	0.460000	0.39030	ACC		TCGA-IB-7887-01A-11D-2154-08	KRT31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257286.1	0	0	1	83	528	0	88		0	0	0	0	88	2		0	0	0	0	0	2	1	1.000000	82	514	0	88	2		0	0	0	0	88	2	-20.000000	1	1	0	0		1	0	0	0	2.045882	0	0.270000	1.780000	0.262030	0.990000	0.800000	1.000000	1.000000	0.959288	0.990000	1	8.900000e-01	1
TP53	7157	broad.mit.edu	37	17	7578206	7578206	+	Missense_Mutation	SNP	T	T	C			TCGA-IB-7887-01A-11D-2154-08	TCGA-IB-7887-10A-01D-2154-08			T	C	T	T		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	35c4c115-e867-4ae4-987f-9ff02003be62	73139364-4a90-4b65-82fb-efa77a95b3fa	g.chr17:7578206T>C	ENST00000269305.4	-	6	832	c.643A>G	c.(643-645)Agt>Ggt	p.S215G	TP53_ENST00000445888.2_Missense_Mutation_p.S215G|TP53_ENST00000574684.1_Intron|TP53_ENST00000455263.2_Missense_Mutation_p.S215G|TP53_ENST00000420246.2_Missense_Mutation_p.S215G|TP53_ENST00000359597.4_Missense_Mutation_p.S215G|TP53_ENST00000413465.2_Missense_Mutation_p.S215G	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	p.0?(8)|p.S215G(6)|p.?(5)|p.S215C(5)|p.H214fs*5(2)|p.S215R(2)|p.D208fs*1(1)|p.R213_S215>X(1)|p.S215fs*32(1)|p.R209fs*6(1)|p.T211fs*28(1)|p.S215fs*31(1)|p.D207_V216del10(1)|p.S215fs*27(1)|p.H214fs*7(1)|p.R213fs*32(1)|p.T211_S215delTFRHS(1)|p.H214_S215insX(1)|p.S215del(1)|p.S215fs*29(1)|p.D208_V216delDRNTFRHSV(1)		24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		Acetylsalicylic acid(DB00945)	ACCACCACACTATGTCGAAAA	0.537000		111	Mis, N, F		breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types	breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		L, E, M, O	43	Substitution - Missense(13)|Deletion - Frameshift(11)|Whole gene deletion(8)|Unknown(5)|Deletion - In frame(4)|Insertion - In frame(1)|Complex - deletion inframe(1)						SO:0001583	missense	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	ENST00000269305.4	1	1	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	T	22.3	4.274381	0.80580	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	D;D;D;D;D;D;D;D	0.99851	-7.17;-7.17;-7.17;-7.17;-7.17;-7.17;-7.17;-7.17	5.28	4.18	0.49190	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99851	0.9931	M	0.90705	3.14	0.58432	D	0.999999	D;D;D;D;D;D;D	0.89917	1.0;1.0;0.999;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	0.995;1.0;0.98;0.996;1.0;1.0;0.999	D	0.97163	0.9839	10	0.87932	D	0	-18.3023	10.6958	0.45899	0.0:0.0:0.1605:0.8394	.	176;215;215;122;215;215;215	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	G	215;215;215;215;215;215;204;122;83;122;83	ENSP00000410739:S215G;ENSP00000352610:S215G;ENSP00000269305:S215G;ENSP00000398846:S215G;ENSP00000391127:S215G;ENSP00000391478:S215G;ENSP00000425104:S83G;ENSP00000423862:S122G	ENSP00000269305:S215G	S	-	1	0	TP53	7518931	1.000000	0.71417	0.471000	0.27229	0.962000	0.63368	6.146000	0.71777	0.919000	0.36945	0.460000	0.39030	AGT		TCGA-IB-7887-01A-11D-2154-08	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	1	0	1	36	217	0	42	1	9.999603e-01	64	32	0	42	2	1	1	134	654	0	1530	2	1	1.000000	35	208	0	42	2		0	0	0	0	42	2	-20.000000	1	1	0	0		1	0	1	1	1.788086	1	0.270000	1.780000	0.156069	0.850000	0.630000	0.990000	0.890000	0.851546	0.850000	1	7.400000e-01	9.500000e-01
UNC13A	23025	broad.mit.edu	37	19	17760372	17760372	+	Silent	SNP	G	G	A			TCGA-IB-7887-01A-11D-2154-08	TCGA-IB-7887-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35c4c115-e867-4ae4-987f-9ff02003be62	73139364-4a90-4b65-82fb-efa77a95b3fa	g.chr19:17760372G>A	ENST00000519716.2	-	13	1463	c.1464C>T	c.(1462-1464)atC>atT	p.I488I	UNC13A_ENST00000551649.1_Silent_p.I488I|UNC13A_ENST00000252773.7_Silent_p.I488I|UNC13A_ENST00000552293.1_Silent_p.I488I|UNC13A_ENST00000550896.1_Silent_p.I488I|UNC13A_ENST00000428389.2_Silent_p.I576I	NM_001080421.2	NP_001073890.2	Q9UPW8	UN13A_HUMAN	unc-13 homolog A (C. elegans)	p.I488I(1)|p.I576I(1)		61					GCATGCTGTCGATGATGATGA	0.567000																								2	Substitution - coding silent(2)						SO:0001819	synonymous_variant			ENST00000519716.2	1	1	hg19	CCDS46013.2																																																																																				TCGA-IB-7887-01A-11D-2154-08	UNC13A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376169.2	1	0	1	82	584	1	119		0	0	0	1	119	2		0	0	0	0	0	2	1	1.000000	81	575	1	118	19		0	0	0	1	119	2	-20.000000	1	1	0	0		1	0	0	0	2.033670	0	0.270000	1.780000	0.257979	0.890000	0.720000	1.000000	1.000000	0.894076	0.890000	1	8.000000e-01	9.900000e-01
MBOAT7	79143	broad.mit.edu	37	19	54691118	54691118	+	Silent	SNP	G	G	A			TCGA-IB-7887-01A-11D-2154-08	TCGA-IB-7887-10A-01D-2154-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	35c4c115-e867-4ae4-987f-9ff02003be62	73139364-4a90-4b65-82fb-efa77a95b3fa	g.chr19:54691118G>A	ENST00000245615.1	-	4	738	c.258C>T	c.(256-258)ttC>ttT	p.F86F	MBOAT7_ENST00000338624.6_Intron|MBOAT7_ENST00000391754.1_Silent_p.F86F|MBOAT7_ENST00000431666.2_Intron|MBOAT7_ENST00000474910.1_5'UTR	NM_024298.3	NP_077274.3	Q96N66	MBOA7_HUMAN	membrane bound O-acyltransferase domain containing 7			10	all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)				TGAGGGCTCGGAAGAACAGGA	0.642000													NSCLC(97;826 2151 10470 22540)											0							SO:0001819	synonymous_variant			ENST00000245615.1	0	1	hg19	CCDS12883.1																																																																																				TCGA-IB-7887-01A-11D-2154-08	MBOAT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142203.1	1	0	0	13	77	0	11	1	9.999996e-01	66	137	0	11	2		0	0	0	0	0	2	1	0.999339	12	69	0	11	2		0	0	0	0	11	2	-19.995520	1	1	0	0		1	0	1	1	2.058955	0	0.270000	1.780000	0.269013	0.990000	0.610000	1.000000	1.000000	0.936127	0.990000	1	8.200000e-01	1
FBN3	84467	broad.mit.edu	37	19	8130859	8130859	+	Nonsense_Mutation	SNP	G	G	A			TCGA-IB-7887-01A-11D-2154-08	TCGA-IB-7887-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35c4c115-e867-4ae4-987f-9ff02003be62	73139364-4a90-4b65-82fb-efa77a95b3fa	g.chr19:8130859G>A	ENST00000600128.1	-	64	8788	c.8374C>T	c.(8374-8376)Cag>Tag	p.Q2792*	FBN3_ENST00000601739.1_Nonsense_Mutation_p.Q2792*|FBN3_ENST00000270509.2_Nonsense_Mutation_p.Q2792*			Q75N90	FBN3_HUMAN	fibrillin 3			132					GGCCCTGGCTGCCCCTCTGGC	0.687000																								0							SO:0001587	stop_gained			ENST00000600128.1	0	1	hg19	CCDS12196.1	.	.	.	.	.	.	.	.	.	.	G	48	14.127981	0.99781	.	.	ENSG00000142449	ENST00000270509;ENST00000341066	.	.	.	3.83	-4.06	0.03986	.	0.602780	0.16277	U	0.221518	.	.	.	.	.	.	0.37599	D	0.920499	.	.	.	.	.	.	.	.	.	.	0.49607	T	0.09	.	9.7216	0.40306	0.5538:0.0:0.4462:0.0	.	.	.	.	X	2792;855	.	ENSP00000270509:Q2792X	Q	-	1	0	FBN3	8036859	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.106000	0.15354	-0.844000	0.04184	-0.768000	0.03414	CAG		TCGA-IB-7887-01A-11D-2154-08	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	1	0	1	44	313	0	61		0	0	0	0	61	2		0	0	0	0	0	2	1	1.000000	43	303	0	60	2		0	0	0	0	61	2	-20.000000	1	1	0	0		1	0	0	0	2.045320	0	0.270000	1.780000	0.262030	0.890000	0.670000	1.000000	1.000000	0.892067	0.890000	1	7.700000e-01	1
FLG	2312	broad.mit.edu	37	1	152277769	152277769	+	Missense_Mutation	SNP	A	A	C	rs143183339		TCGA-IB-7887-01A-11D-2154-08	TCGA-IB-7887-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35c4c115-e867-4ae4-987f-9ff02003be62	73139364-4a90-4b65-82fb-efa77a95b3fa	g.chr1:152277769A>C	ENST00000368799.1	-	3	9628	c.9593T>G	c.(9592-9594)gTc>gGc	p.V3198G	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin			424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)		TTGTCCCTGGACTGCCTGTGA	0.552000									Ichthyosis															0							SO:0001583	missense	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	ENST00000368799.1	1	1	hg19	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	C	1.935	-0.444964	0.04604	4.54E-4	0.0	ENSG00000143631	ENST00000368799	T	0.01963	4.53	1.93	-1.78	0.07957	.	.	.	.	.	T	0.00144	0.0004	N	0.00347	-1.61	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.32402	-0.9908	9	0.10636	T	0.68	.	0.4443	0.00491	0.198:0.336:0.196:0.27	.	3198	P20930	FILA_HUMAN	G	3198	ENSP00000357789:V3198G	ENSP00000357789:V3198G	V	-	2	0	FLG	150544393	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.291000	0.08343	-0.950000	0.03659	-0.383000	0.06682	GTC		TCGA-IB-7887-01A-11D-2154-08	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	1	0	0	209	1382	0	242		0	0	0	0	242	2		0	0	0	0	0	2	1	1.000000	194	1276	0	333	2		0	0	0	0	242	2	-20.000000	1	1	121402	17	46	1	0	0	0	2.052197	0	0.270000	1.780000	0.266037	0.960000	0.840000	1.000000	1.000000	0.956658	0.960000	1	9.000000e-01	1
OR10K2	391107	broad.mit.edu	37	1	158390039	158390039	+	Silent	SNP	G	G	A			TCGA-IB-7887-01A-11D-2154-08	TCGA-IB-7887-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35c4c115-e867-4ae4-987f-9ff02003be62	73139364-4a90-4b65-82fb-efa77a95b3fa	g.chr1:158390039G>A	ENST00000314902.2	-	1	617	c.618C>T	c.(616-618)gtC>gtT	p.V206V		NM_001004476.1	NP_001004476.1	Q6IF99	O10K2_HUMAN	olfactory receptor, family 10, subfamily K, member 2			36	all_hematologic(112;0.0378)				GGATAGCCAGGACCAATGTAC	0.443000																								0							SO:0001819	synonymous_variant			ENST00000314902.2	1	1	hg19	CCDS30896.1																																																																																				TCGA-IB-7887-01A-11D-2154-08	OR10K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051854.1	1	0	1	45	391	0	75		0	0	0	0	75	2		0	0	0	0	0	2	1	1.000000	45	376	0	75	2		0	0	0	0	75	2	-20.000000	1	1	0	0		1	0	0	0	2.052197	0	0.270000	1.780000	0.266037	0.750000	0.560000	0.970000	0.760000	0.767868	0.750000	0	6.500000e-01	8.700000e-01
TAF5L	27097	broad.mit.edu	37	1	229730411	229730411	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-7887-01A-11D-2154-08	TCGA-IB-7887-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35c4c115-e867-4ae4-987f-9ff02003be62	73139364-4a90-4b65-82fb-efa77a95b3fa	g.chr1:229730411C>T	ENST00000366676.1	-	4	1402	c.1403G>A	c.(1402-1404)cGt>cAt	p.R468H	TAF5L_ENST00000258281.2_Missense_Mutation_p.R468H			O75529	TAF5L_HUMAN	TAF5-like RNA polymerase II, p300/CBP-associated factor (PCAF)-associated factor, 65kDa	p.R468P(1)		11	Breast(184;0.193)|Ovarian(103;0.249)	Prostate(94;0.167)			CACGGGGCCACGGTGGCCTGT	0.607000																								1	Substitution - Missense(1)						SO:0001583	missense			ENST00000366676.1	1	1	hg19	CCDS1581.1	.	.	.	.	.	.	.	.	.	.	C	12.60	1.987862	0.35036	.	.	ENSG00000135801	ENST00000366676;ENST00000258281	T;T	0.60548	0.18;0.18	5.97	5.06	0.68205	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.047962	0.85682	D	0.000000	T	0.45935	0.1367	N	0.21097	0.63	0.80722	D	1	B	0.15473	0.013	B	0.10450	0.005	T	0.37407	-0.9707	10	0.54805	T	0.06	-7.1912	15.1546	0.72730	0.0:0.9326:0.0:0.0674	.	468	O75529	TAF5L_HUMAN	H	468	ENSP00000355636:R468H;ENSP00000258281:R468H	ENSP00000258281:R468H	R	-	2	0	TAF5L	227797034	1.000000	0.71417	0.921000	0.36526	0.013000	0.08279	7.785000	0.85724	1.537000	0.49254	0.655000	0.94253	CGT		TCGA-IB-7887-01A-11D-2154-08	TAF5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095229.1	1	0	1	52	760	0	107	1	8.652265e-01	10	44	0	107	2		0	0	0	0	0	2	1	1.000000	52	752	0	106	2		0	0	0	0	107	2	-9.415912	1	1	0	0		1	0	1	1	2.057782	0	0.270000	1.780000	0.268024	0.470000	0.350000	0.600000	0.470000	0.479382	0.470000	0	4.100000e-01	5.400000e-01
TFB2M	64216	broad.mit.edu	37	1	246704361	246704361	+	Missense_Mutation	SNP	A	A	T			TCGA-IB-7887-01A-11D-2154-08	TCGA-IB-7887-10A-01D-2154-08			A	T	A	A		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	35c4c115-e867-4ae4-987f-9ff02003be62	73139364-4a90-4b65-82fb-efa77a95b3fa	g.chr1:246704361A>T	ENST00000366514.4	-	8	1348	c.1163T>A	c.(1162-1164)cTg>cAg	p.L388Q		NM_022366.2	NP_071761.1	Q9H5Q4	TFB2M_HUMAN	transcription factor B2, mitochondrial			28	all_cancers(71;4.25e-05)|all_epithelial(71;4.92e-06)|Ovarian(71;0.0254)|all_lung(81;0.0272)|Breast(184;0.0318)|Lung NSC(105;0.0376)		OV - Ovarian serous cystadenocarcinoma(106;0.00358)		TTCATCATACAGCCATTTATA	0.373000																								0							SO:0001583	missense			ENST00000366514.4	1	1	hg19	CCDS1627.1	.	.	.	.	.	.	.	.	.	.	A	14.54	2.567021	0.45694	.	.	ENSG00000162851	ENST00000366514	T	0.40476	1.03	5.23	5.23	0.72850	.	0.173798	0.38837	N	0.001547	T	0.56411	0.1983	L	0.54323	1.7	0.80722	D	1	D	0.89917	1.0	D	0.63597	0.916	T	0.59883	-0.7370	10	0.87932	D	0	-0.8824	12.7768	0.57453	1.0:0.0:0.0:0.0	.	388	Q9H5Q4	TFB2M_HUMAN	Q	388	ENSP00000355471:L388Q	ENSP00000355471:L388Q	L	-	2	0	TFB2M	244770984	0.993000	0.37304	0.292000	0.24919	0.018000	0.09664	4.722000	0.61958	2.108000	0.64289	0.528000	0.53228	CTG		TCGA-IB-7887-01A-11D-2154-08	TFB2M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096673.1	1	0	1	50	380	0	62	1	9.999654e-01	40	76	0	62	2		0	0	0	0	0	2	1	1.000000	50	375	0	62	2		0	0	0	0	62	2	-18.936130	1	1	0	0		1	0	1	1	2.056446	0	0.270000	1.780000	0.268024	0.850000	0.650000	1.000000	1.000000	0.858840	0.850000	1	7.400000e-01	9.800000e-01
RRAGC	64121	broad.mit.edu	37	1	39305328	39305328	+	Missense_Mutation	SNP	A	A	C			TCGA-IB-7887-01A-11D-2154-08	TCGA-IB-7887-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35c4c115-e867-4ae4-987f-9ff02003be62	73139364-4a90-4b65-82fb-efa77a95b3fa	g.chr1:39305328A>C	ENST00000373001.3	-	7	1273	c.1097T>G	c.(1096-1098)gTt>gGt	p.V366G	RRAGC_ENST00000474456.1_5'UTR	NM_022157.2	NP_071440.1			Ras-related GTP binding C			10	Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)			CACCTCAAAAACCTCATGAAT	0.458000																								0							SO:0001583	missense			ENST00000373001.3	0	1	hg19	CCDS430.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.082251	0.76528	.	.	ENSG00000116954	ENST00000373001	.	.	.	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	D	0.85013	0.5600	M	0.90309	3.105	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.999	D;D;D	0.76071	0.987;0.944;0.979	D	0.87774	0.2607	9	0.62326	D	0.03	-33.3787	16.2355	0.82371	1.0:0.0:0.0:0.0	.	332;300;366	E7ENI3;D3DPT8;Q9HB90	.;.;RRAGC_HUMAN	G	366	.	ENSP00000362092:V366G	V	-	2	0	RRAGC	39077915	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.339000	0.96797	2.238000	0.73509	0.533000	0.62120	GTT		TCGA-IB-7887-01A-11D-2154-08	RRAGC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001222.2	0	0	0	15	405	1	49	0	3.517657e-02	0	123	1	49	10		0	0	0	0	0	2	0	0.063780	15	398	1	49	25		0	0	0	1	49	2	-15.126710	1	1	0	0		1	1	2	3	2.067602	0	0.270000	1.780000	0.271966	0.270000	0.150000	0.450000	0.260000	0.286871	0.270000	0	2.000000e-01	3.500000e-01
ZYG11B	79699	broad.mit.edu	37	1	53287249	53287249	+	Missense_Mutation	SNP	G	G	A	rs151077871		TCGA-IB-7887-01A-11D-2154-08	TCGA-IB-7887-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35c4c115-e867-4ae4-987f-9ff02003be62	73139364-4a90-4b65-82fb-efa77a95b3fa	g.chr1:53287249G>A	ENST00000294353.6	+	14	2328	c.2183G>A	c.(2182-2184)cGc>cAc	p.R728H	ZYG11B_ENST00000443756.2_Missense_Mutation_p.R658H	NM_024646.2	NP_078922.1	Q9C0D3	ZY11B_HUMAN	zyg-11 family member B, cell cycle regulator			30					CACATTGTGCGCCATGGGAGG	0.418000																								0							SO:0001583	missense			ENST00000294353.6	1	1	hg19	CCDS30717.1	.	.	.	.	.	.	.	.	.	.	G	18.24	3.579177	0.65878	2.27E-4	0.0	ENSG00000162378	ENST00000443756;ENST00000294353	T	0.47177	0.85	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	T	0.37046	0.0989	L	0.51422	1.61	0.80722	D	1	P;B	0.39601	0.68;0.07	B;B	0.26094	0.066;0.019	T	0.35525	-0.9785	10	0.48119	T	0.1	.	12.6624	0.56822	0.0756:0.0:0.9244:0.0	.	658;728	B4DK95;Q9C0D3	.;ZY11B_HUMAN	H	658;728	ENSP00000294353:R728H	ENSP00000294353:R728H	R	+	2	0	ZYG11B	53059837	1.000000	0.71417	0.997000	0.53966	0.997000	0.91878	5.446000	0.66600	2.567000	0.86603	0.591000	0.81541	CGC		TCGA-IB-7887-01A-11D-2154-08	ZYG11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024749.1	1	0	1	46	322	0	70	1	5.009208e-01	4	9	0	70	2		0	0	0	0	0	2	1	1.000000	45	318	0	70	2		0	0	0	0	70	2	-3.318834	1	1	121412	2	33	1	1	2	3	2.067602	0	0.270000	1.780000	0.271966	0.920000	0.690000	1.000000	1.000000	0.911345	0.920000	1	8.000000e-01	1
DLGAP4	22839	broad.mit.edu	37	20	35060133	35060133	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-7887-01A-11D-2154-08	TCGA-IB-7887-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35c4c115-e867-4ae4-987f-9ff02003be62	73139364-4a90-4b65-82fb-efa77a95b3fa	g.chr20:35060133G>A	ENST00000373907.2	+	2	212	c.13G>A	c.(13-15)Ggt>Agt	p.G5S	DLGAP4_ENST00000373913.3_Missense_Mutation_p.G5S|DLGAP4_ENST00000401952.2_Missense_Mutation_p.G5S|DLGAP4_ENST00000339266.5_Missense_Mutation_p.G5S			Q9Y2H0	DLGP4_HUMAN	discs, large (Drosophila) homolog-associated protein 4			37	Breast(12;0.0192)	Myeloproliferative disorder(115;0.00878)			GAAAGGCCTCGGTGACAGCCG	0.692000																								0							SO:0001583	missense			ENST00000373907.2	1	1	hg19		.	.	.	.	.	.	.	.	.	.	G	11.48	1.651735	0.29336	.	.	ENSG00000080845	ENST00000373913;ENST00000401952;ENST00000373907;ENST00000339266	T;T;T;T	0.48522	0.81;0.81;0.81;0.81	5.67	3.36	0.38483	.	0.151756	0.64402	D	0.000016	T	0.45438	0.1342	N	0.19112	0.55	0.44852	D	0.997862	D	0.89917	1.0	D	0.91635	0.999	T	0.39165	-0.9627	10	0.02654	T	1	.	11.4918	0.50385	0.0787:0.1303:0.7911:0.0	.	5	Q9Y2H0-1	.	S	5	ENSP00000363023:G5S;ENSP00000384954:G5S;ENSP00000363014:G5S;ENSP00000341633:G5S	ENSP00000341633:G5S	G	+	1	0	DLGAP4	34493547	1.000000	0.71417	0.994000	0.49952	0.997000	0.91878	5.453000	0.66645	1.377000	0.46286	0.561000	0.74099	GGT		TCGA-IB-7887-01A-11D-2154-08	DLGAP4-007	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000079025.2	1	0	0	44	302	0	41		0	0	0	0	41	2		0	0	0	0	0	2	1	1.000000	41	288	0	39	2		0	0	0	0	41	2	-3.221981	1	1	120658	5	36	1	0	0	0	2.051649	0	0.270000	1.780000	0.266037	0.930000	0.690000	1.000000	1.000000	0.914925	0.930000	1	8.000000e-01	1
SEMG2	6407	broad.mit.edu	37	20	43851593	43851593	+	Missense_Mutation	SNP	G	G	C			TCGA-IB-7887-01A-11D-2154-08	TCGA-IB-7887-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35c4c115-e867-4ae4-987f-9ff02003be62	73139364-4a90-4b65-82fb-efa77a95b3fa	g.chr20:43851593G>C	ENST00000372769.3	+	2	1410	c.1320G>C	c.(1318-1320)gaG>gaC	p.E440D		NM_003008.2	NP_002999.1	Q02383	SEMG2_HUMAN	semenogelin II			36		Myeloproliferative disorder(115;0.0122)			AAACTGAAGAGAAAATACATG	0.383000																								0							SO:0001583	missense			ENST00000372769.3	1	1	hg19	CCDS13346.1	.	.	.	.	.	.	.	.	.	.	G	5.930	0.355577	0.11239	.	.	ENSG00000124157	ENST00000372769	T	0.10005	2.92	1.03	-1.67	0.08238	.	.	.	.	.	T	0.14141	0.0342	L	0.27053	0.805	0.09310	N	1	P;B	0.51057	0.941;0.004	D;B	0.71414	0.973;0.012	T	0.18209	-1.0344	9	0.41790	T	0.15	.	3.074	0.06240	0.0:0.2992:0.3985:0.3023	.	440;440	A8K6Z6;Q02383	.;SEMG2_HUMAN	D	440	ENSP00000361855:E440D	ENSP00000361855:E440D	E	+	3	2	SEMG2	43285007	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.388000	0.07352	-0.534000	0.06315	-1.468000	0.01013	GAG		TCGA-IB-7887-01A-11D-2154-08	SEMG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079417.1	1	0	1	87	525	0	87		0	0	0	0	87	2		0	0	0	0	0	2	1	1.000000	86	510	0	87	2		0	0	0	0	87	2	-20.000000	1	1	0	0		1	0	0	0	2.051649	0	0.270000	1.780000	0.266037	0.990000	0.850000	1.000000	1.000000	0.979746	0.990000	1	9.400000e-01	1
TTC3	7267	broad.mit.edu	37	21	38572533	38572533	+	Splice_Site	SNP	G	G	A			TCGA-IB-7887-01A-11D-2154-08	TCGA-IB-7887-10A-01D-2154-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	35c4c115-e867-4ae4-987f-9ff02003be62	73139364-4a90-4b65-82fb-efa77a95b3fa	g.chr21:38572533G>A	ENST00000399017.2	+	45	8598	c.5851G>A	c.(5851-5853)Gca>Aca	p.A1951T	TTC3_ENST00000355666.1_Splice_Site_p.A1951T|TTC3_ENST00000354749.2_Splice_Site_p.A1951T|TTC3_ENST00000479930.1_3'UTR	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3			75		Myeloproliferative disorder(46;0.0412)			GTTTCCACAGGCACTGGGTGC	0.428000													Ovarian(38;194 1649 35661)											0							SO:0001630	splice_region_variant			ENST00000399017.2	1	0	hg19	CCDS13651.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	3.961|3.961	-0.010251|-0.010251	0.07727|0.07727	.|.	.|.	ENSG00000182670|ENSG00000182670	ENST00000355666;ENST00000399017;ENST00000354749|ENST00000428693	T;T;T|.	0.08807|.	3.05;3.05;3.05|.	5.58|5.58	1.74|1.74	0.24563|0.24563	.|.	0.905217|.	0.09312|.	N|.	0.819490|.	T|T	0.45776|0.45776	0.1359|0.1359	L|L	0.46157|0.46157	1.445|1.445	0.58432|0.58432	D|D	0.999999|0.999999	B|.	0.18461|.	0.028|.	B|.	0.12837|.	0.008|.	T|T	0.25398|0.25398	-1.0133|-1.0133	9|5	.|.	.|.	.|.	-0.7948|-0.7948	3.6024|3.6024	0.08030|0.08030	0.2713:0.0:0.553:0.1756|0.2713:0.0:0.553:0.1756	.|.	1951|.	P53804|.	TTC3_HUMAN|.	T|Y	1951|242	ENSP00000347889:A1951T;ENSP00000381981:A1951T;ENSP00000346791:A1951T|.	.|.	A|C	+|+	1|2	0|0	TTC3|TTC3	37494403|37494403	0.258000|0.258000	0.24033|0.24033	0.448000|0.448000	0.26945|0.26945	0.031000|0.031000	0.12232|0.12232	0.312000|0.312000	0.19397|0.19397	0.303000|0.303000	0.22785|0.22785	-0.182000|-0.182000	0.12963|0.12963	GCA|TGC		TCGA-IB-7887-01A-11D-2154-08	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1	1	0	1	24	215	0	29	1	9.999399e-01	39	103	0	29	2		0	0	0	0	0	2	1	1.000000	23	210	0	29	2		0	0	0	0	29	2	-20.000000	1	1	0	0		1	0	1	1	1.781476	1	0.270000	1.780000	0.157384	0.630000	0.420000	0.880000	0.630000	0.649148	0.630000	0	5.200000e-01	7.700000e-01
PES1	23481	broad.mit.edu	37	22	30983324	30983324	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-7887-01A-11D-2154-08	TCGA-IB-7887-10A-01D-2154-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	35c4c115-e867-4ae4-987f-9ff02003be62	73139364-4a90-4b65-82fb-efa77a95b3fa	g.chr22:30983324C>T	ENST00000354694.7	-	4	423	c.317G>A	c.(316-318)cGt>cAt	p.R106H	PES1_ENST00000405677.1_5'UTR|PES1_ENST00000335214.6_Missense_Mutation_p.R106H|PES1_ENST00000402284.3_Missense_Mutation_p.R106H|PES1_ENST00000402281.1_5'UTR	NM_001243225.1|NM_014303.3	NP_001230154.1|NP_055118.1			pescadillo ribosomal biogenesis factor 1			29					GTCCTTTAAACGCTCTACAGT	0.498000																								0							SO:0001583	missense			ENST00000354694.7	1	1	hg19	CCDS13880.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.272796	0.80580	.	.	ENSG00000100029	ENST00000354694;ENST00000402284;ENST00000335214;ENST00000433575	T;T;T;T	0.48201	0.82;0.82;0.82;0.82	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	T	0.51736	0.1692	M	0.75085	2.285	0.80722	D	1	B;B;B;B	0.32245	0.361;0.25;0.14;0.361	B;B;B;B	0.28232	0.041;0.087;0.024;0.041	T	0.55147	-0.8186	10	0.54805	T	0.06	-9.5911	19.2042	0.93723	0.0:1.0:0.0:0.0	.	106;106;106;106	B2RDF2;B5MCF9;O00541-2;O00541	.;.;.;PESC_HUMAN	H	106	ENSP00000346725:R106H;ENSP00000384252:R106H;ENSP00000334612:R106H;ENSP00000388071:R106H	ENSP00000334612:R106H	R	-	2	0	PES1	29313324	1.000000	0.71417	0.990000	0.47175	0.937000	0.57800	7.192000	0.77771	2.650000	0.89964	0.655000	0.94253	CGT		TCGA-IB-7887-01A-11D-2154-08	PES1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321188.3	1	0	1	65	406	0	62	1	1	56	115	0	62	2		0	0	0	0	0	2	1	1.000000	65	393	0	62	2		0	0	0	0	62	2	-20.000000	1	1	121412	2	35	1	1	2	3	2.066540	0	0.270000	1.780000	0.271966	0.990000	0.800000	1.000000	1.000000	0.967455	0.990000	1	9.000000e-01	1
LRCH3	84859	broad.mit.edu	37	3	197553808	197553808	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-7887-01A-11D-2154-08	TCGA-IB-7887-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35c4c115-e867-4ae4-987f-9ff02003be62	73139364-4a90-4b65-82fb-efa77a95b3fa	g.chr3:197553808C>T	ENST00000425562.2	+	5	700	c.700C>T	c.(700-702)Cct>Tct	p.P234S	LRCH3_ENST00000536618.1_5'Flank|LRCH3_ENST00000334859.4_Missense_Mutation_p.P234S|LRCH3_ENST00000438796.2_Missense_Mutation_p.P234S|LRCH3_ENST00000414675.2_Missense_Mutation_p.P234S|LRCH3_ENST00000441090.2_Missense_Mutation_p.P108S			Q96II8	LRCH3_HUMAN	leucine-rich repeats and calponin homology (CH) domain containing 3			29	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;4.82e-24)|all cancers(36;3.61e-22)|OV - Ovarian serous cystadenocarcinoma(49;7.08e-19)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)		TACCACAATCCCTGTTTGTTA	0.423000																								0							SO:0001583	missense			ENST00000425562.2	0	1	hg19		.	.	.	.	.	.	.	.	.	.	C	33	5.261561	0.95368	.	.	ENSG00000186001	ENST00000438796;ENST00000441090;ENST00000414675;ENST00000334859;ENST00000425562	T;T;T;T;T	0.59502	1.85;0.26;1.85;1.85;1.85	5.31	5.31	0.75309	.	0.000000	0.85682	D	0.000000	T	0.78773	0.4336	M	0.81614	2.55	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;0.997	D;D;D;D	0.97110	1.0;1.0;1.0;0.966	T	0.81291	-0.0999	10	0.87932	D	0	-15.0214	19.3993	0.94621	0.0:1.0:0.0:0.0	.	108;234;234;234	E9PD99;B4E0T7;Q96II8-2;Q96II8-3	.;.;.;.	S	234;108;234;234;234	ENSP00000399751:P234S;ENSP00000394609:P108S;ENSP00000394965:P234S;ENSP00000334375:P234S;ENSP00000393579:P234S	ENSP00000334375:P234S	P	+	1	0	LRCH3	199038205	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.421000	0.80204	2.654000	0.90174	0.650000	0.86243	CCT		TCGA-IB-7887-01A-11D-2154-08	LRCH3-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000339965.1	0	0	1	28	475	1	70	1	2.043922e-01	9	45	1	70	5		0	0	0	0	0	2	1	0.817563	28	462	1	69	22		0	0	0	1	70	2	-2.619927	1	1	0	0		1	1	2	3	2.341094	1	0.270000	1.780000	0.356828	0.470000	0.310000	0.650000	0.460000	0.481075	0.470000	0	3.800000e-01	5.600000e-01
DGKB	1607	broad.mit.edu	37	7	14724956	14724956	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-7887-01A-11D-2154-08	TCGA-IB-7887-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35c4c115-e867-4ae4-987f-9ff02003be62	73139364-4a90-4b65-82fb-efa77a95b3fa	g.chr7:14724956C>T	ENST00000403951.2	-	10	1162	c.743G>A	c.(742-744)cGa>cAa	p.R248Q	DGKB_ENST00000258767.5_Missense_Mutation_p.R248Q|DGKB_ENST00000403963.1_5'UTR|DGKB_ENST00000402815.1_Missense_Mutation_p.R248Q|DGKB_ENST00000406247.3_Missense_Mutation_p.R248Q|DGKB_ENST00000407950.1_Missense_Mutation_p.R241Q|DGKB_ENST00000444700.2_Missense_Mutation_p.R241Q|DGKB_ENST00000399322.3_Missense_Mutation_p.R248Q			Q9Y6T7	DGKB_HUMAN	diacylglycerol kinase, beta 90kDa			72					GTGCTTCAGTCGCCACACGTG	0.463000																								0							SO:0001583	missense			ENST00000403951.2	1	1	hg19	CCDS47547.1	.	.	.	.	.	.	.	.	.	.	C	36	5.902986	0.97087	.	.	ENSG00000136267	ENST00000403951;ENST00000399322;ENST00000258767;ENST00000402815;ENST00000407950;ENST00000444700;ENST00000406247	D;D;D;D;D;D;D	0.92647	-3.08;-3.08;-3.08;-3.08;-3.08;-3.08;-3.08	6.16	6.16	0.99307	Protein kinase C-like, phorbol ester/diacylglycerol binding (4);	0.052374	0.64402	D	0.000001	D	0.94683	0.8285	L	0.43701	1.375	0.58432	D	0.999999	D;D;D;D	0.89917	0.999;0.995;0.995;1.0	D;P;P;D	0.70227	0.943;0.876;0.876;0.968	D	0.93847	0.7142	10	0.52906	T	0.07	.	20.8598	0.99761	0.0:1.0:0.0:0.0	.	248;241;248;248	B7ZL83;C9JTC0;Q9Y6T7-2;Q9Y6T7	.;.;.;DGKB_HUMAN	Q	248;248;248;248;241;241;248	ENSP00000385780:R248Q;ENSP00000382260:R248Q;ENSP00000258767:R248Q;ENSP00000384909:R248Q;ENSP00000385031:R241Q;ENSP00000388451:R241Q;ENSP00000386066:R248Q	ENSP00000258767:R248Q	R	-	2	0	DGKB	14691481	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.818000	0.86416	2.937000	0.99478	0.650000	0.86243	CGA		TCGA-IB-7887-01A-11D-2154-08	DGKB-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000326356.2	1	0	1	65	326	0	48		0	0	0	0	48	2		0	0	0	0	0	2	1	1.000000	64	322	0	48	2		0	0	0	0	48	2	-3.039706	1	1	0	0		1	0	1	1	2.055534	0	0.270000	1.780000	0.268024	0.990000	0.960000	1.000000	1.000000	0.998013	0.990000	1	9.900000e-01	1
GLI3	2737	broad.mit.edu	37	7	42004926	42004926	+	Missense_Mutation	SNP	A	A	C			TCGA-IB-7887-01A-11D-2154-08	TCGA-IB-7887-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35c4c115-e867-4ae4-987f-9ff02003be62	73139364-4a90-4b65-82fb-efa77a95b3fa	g.chr7:42004926A>C	ENST00000395925.3	-	15	3829	c.3745T>G	c.(3745-3747)Tgt>Ggt	p.C1249G	GLI3_ENST00000479210.1_5'UTR	NM_000168.5	NP_000159.3	P10071	GLI3_HUMAN	GLI family zinc finger 3			112					GGGGCCTTACAGGGCTGTTCA	0.612000									Pallister-Hall syndrome;Greig Cephalopolysyndactyly															0							SO:0001583	missense	Familial Cancer Database	;	ENST00000395925.3	1	1	hg19	CCDS5465.1	.	.	.	.	.	.	.	.	.	.	A	8.711	0.912013	0.17907	.	.	ENSG00000106571	ENST00000395925	T	0.12465	2.68	5.8	3.26	0.37387	.	0.934476	0.09053	N	0.855569	T	0.12475	0.0303	L	0.49126	1.545	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.19451	-1.0305	10	0.26408	T	0.33	.	5.4414	0.16511	0.4156:0.3209:0.0:0.2635	.	1249	P10071	GLI3_HUMAN	G	1249	ENSP00000379258:C1249G	ENSP00000379258:C1249G	C	-	1	0	GLI3	41971451	0.095000	0.21747	0.036000	0.18154	0.117000	0.20001	1.910000	0.39927	2.209000	0.71365	0.533000	0.62120	TGT		TCGA-IB-7887-01A-11D-2154-08	GLI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250806.3	1	0	1	65	513	0	99	0	6.186468e-01	0	18	0	99	2		0	0	0	0	0	2	1	1.000000	64	504	0	99	2		0	0	0	0	99	2	-20.000000	1	1	0	0		1	0	1	1	2.055534	0	0.270000	1.780000	0.268024	0.820000	0.650000	1.000000	1.000000	0.834291	0.820000	0	7.300000e-01	9.300000e-01
GLI3	2737	broad.mit.edu	37	7	42004927	42004927	+	Silent	SNP	G	G	A			TCGA-IB-7887-01A-11D-2154-08	TCGA-IB-7887-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35c4c115-e867-4ae4-987f-9ff02003be62	73139364-4a90-4b65-82fb-efa77a95b3fa	g.chr7:42004927G>A	ENST00000395925.3	-	15	3828	c.3744C>T	c.(3742-3744)ccC>ccT	p.P1248P	GLI3_ENST00000479210.1_5'UTR	NM_000168.5	NP_000159.3	P10071	GLI3_HUMAN	GLI family zinc finger 3			112					GGGCCTTACAGGGCTGTTCAT	0.617000									Pallister-Hall syndrome;Greig Cephalopolysyndactyly															0							SO:0001819	synonymous_variant	Familial Cancer Database	;	ENST00000395925.3	1	1	hg19	CCDS5465.1																																																																																				TCGA-IB-7887-01A-11D-2154-08	GLI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250806.3	0	0	1	65	518	0	98	0	6.718914e-01	0	20	0	98	2		0	0	0	0	0	2	1	1.000000	65	508	0	98	2		0	0	0	0	98	2	-2.598634	1	1	121412	1	31	1	0	1	1	2.055534	0	0.270000	1.780000	0.268024	0.820000	0.640000	1.000000	1.000000	0.827592	0.820000	0	7.200000e-01	9.200000e-01
CLVS1	157807	broad.mit.edu	37	8	62212794	62212794	+	Silent	SNP	C	C	T			TCGA-IB-7887-01A-11D-2154-08	TCGA-IB-7887-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35c4c115-e867-4ae4-987f-9ff02003be62	73139364-4a90-4b65-82fb-efa77a95b3fa	g.chr8:62212794C>T	ENST00000519846.1	+	3	880	c.408C>T	c.(406-408)taC>taT	p.Y136Y	CLVS1_ENST00000518592.1_Intron|RP11-787D18.1_ENST00000518064.1_RNA|CLVS1_ENST00000325897.4_Silent_p.Y136Y|RP11-787D18.1_ENST00000521801.1_RNA			Q8IUQ0	CLVS1_HUMAN	clavesin 1	p.Y136*(1)		41					GAGACCATTACGGCAGGAAGA	0.443000																								1	Substitution - Nonsense(1)						SO:0001819	synonymous_variant			ENST00000519846.1	1	1	hg19	CCDS6176.1																																																																																				TCGA-IB-7887-01A-11D-2154-08	CLVS1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378323.1	1	0	1	45	300	0	50	0	0	0	1	0	50	2		0	0	0	0	0	2	1	1.000000	44	290	0	49	2		0	0	0	0	50	2	-20.000000	1	1	121400	4	35	1	0	1	1	2.056610	0	0.270000	1.780000	0.268024	0.950000	0.710000	1.000000	1.000000	0.931040	0.950000	1	8.300000e-01	1
IGSF1	3547	broad.mit.edu	37	X	130408064	130408064	+	Nonsense_Mutation	SNP	G	G	A			TCGA-IB-7887-01A-11D-2154-08	TCGA-IB-7887-10A-01D-2154-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35c4c115-e867-4ae4-987f-9ff02003be62	73139364-4a90-4b65-82fb-efa77a95b3fa	g.chrX:130408064G>A	ENST00000361420.3	-	19	3947	c.3868C>T	c.(3868-3870)Cga>Tga	p.R1290*	IGSF1_ENST00000370903.3_Nonsense_Mutation_p.R1295*|IGSF1_ENST00000370904.1_Nonsense_Mutation_p.R1281*|IGSF1_ENST00000467244.1_5'Flank|IGSF1_ENST00000370910.1_Nonsense_Mutation_p.R1281*			Q8N6C5	IGSF1_HUMAN	immunoglobulin superfamily, member 1			78					TACCTGGTTCGCAGTCGAGGC	0.502000																								0							SO:0001587	stop_gained			ENST00000361420.3	0	1	hg19	CCDS14629.1	.	.	.	.	.	.	.	.	.	.	G	42	9.400588	0.99159	.	.	ENSG00000147255	ENST00000370910;ENST00000361420;ENST00000370904;ENST00000370903	.	.	.	4.48	4.48	0.54585	.	0.350736	0.21139	N	0.079510	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.4099	0.49919	0.0:0.0:1.0:0.0	.	.	.	.	X	1281;1290;1281;1295	.	ENSP00000355010:R1290X	R	-	1	2	IGSF1	130235745	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	1.588000	0.36633	2.465000	0.83290	0.544000	0.68410	CGA		TCGA-IB-7887-01A-11D-2154-08	IGSF1-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058288.1	1	0	1	263	1495	0	242	1	7.144762e-01	15	1	0	242	2		0	0	0	0	0	2	1	1.000000	250	1450	0	241	2		0	0	0	0	242	2	-20.000000	1	1	121410	2	29	1	0	1	1			0.270000	1.780000	0.270000	0.990000	0.980000	1.000000	1.000000	0.999062	0.990000	1	9.900000e-01	1
