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
CDKN2A	1029	broad.mit.edu	37	9	21971096	21971096	+	Frame_Shift_Del	DEL	C	C	-	rs121913384		TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08			C	-	C	C		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr9:21971096delC	ENST00000304494.5	-	2	532	c.262delG	c.(262-264)gagfs	p.E88fs	CDKN2A_ENST00000530628.2_Frame_Shift_Del_p.G103fs|CDKN2A_ENST00000498124.1_Frame_Shift_Del_p.E88fs|CDKN2A_ENST00000579755.1_Frame_Shift_Del_p.G103fs|CDKN2A_ENST00000494262.1_Frame_Shift_Del_p.E37fs|CDKN2A_ENST00000497750.1_Frame_Shift_Del_p.E37fs|CDKN2A_ENST00000578845.2_Frame_Shift_Del_p.E37fs|CDKN2A_ENST00000446177.1_Frame_Shift_Del_p.E88fs|CDKN2A_ENST00000361570.3_Frame_Shift_Del_p.G144fs|CDKN2A_ENST00000498628.2_Frame_Shift_Del_p.E37fs|CDKN2A_ENST00000579122.1_Frame_Shift_Del_p.E88fs|RP11-145E5.5_ENST00000404796.2_Intron|CDKN2A_ENST00000479692.2_Frame_Shift_Del_p.E37fs	NM_000077.4	NP_000068.1	P42771	CD2A1_HUMAN	cyclin-dependent kinase inhibitor 2A	p.0?(1315)|p.?(44)|p.E88*(15)|p.E88K(3)|p.H83fs*2(2)|p.D84_F90del(1)|p.0(1)|p.V82_G89>G(1)|p.E61_L94del(1)|p.G143V(1)|p.R137fs*48(1)|p.A68fs*3(1)|p.V82_E88del(1)|p.E87K(1)		4199		all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172)			AGGAAGCCCTCCCGGGCAGCG	0.756000	E88*(CAL33_UPPER_AERODIGESTIVE_TRACT)	17								HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07)														1388	Whole gene deletion(1316)|Unknown(44)|Substitution - Nonsense(15)|Substitution - Missense(5)|Deletion - Frameshift(4)|Deletion - In frame(3)|Complex - deletion inframe(1)	GRCh37	CM034218	CDKN2A	M	rs121913384	SO:0001589	frameshift_variant			ENST00000304494.5	1	0	hg19	CCDS6510.1																																																																																				TCGA-YB-A89D-01A-12D-A36O-08	CDKN2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000051915.1	1	0	0	28	128	0	42	1	1	162	272	0	42	2	1	1	41	148	0	175	2	1	0.993169	29	117	1	40	13	0	0	0	0	0	0		-3.465120	1	1	0	0		1	0	2	2	1.716754	1	0.240000	3.280000	0.240000	0.990000	0.990000	1.000000	1.000000	0.998930	0.990000	1	9.900000e-01	1
GRHPR	9380	broad.mit.edu	37	9	37425978	37425978	+	Frame_Shift_Del	DEL	G	G	-			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08			G	-	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr9:37425978delG	ENST00000318158.6	+	3	359	c.274delG	c.(274-276)gaafs	p.E92fs	GRHPR_ENST00000493368.1_3'UTR|GRHPR_ENST00000607784.1_Frame_Shift_Del_p.E92fs	NM_012203.1	NP_036335.1	Q9UBQ7	GRHPR_HUMAN	glyoxylate reductase/hydroxypyruvate reductase			12					GGCTTTGGATGAAATCAAGAA	0.483000																								0							SO:0001589	frameshift_variant			ENST00000318158.6	0	1	hg19	CCDS6609.1																																																																																				TCGA-YB-A89D-01A-12D-A36O-08	GRHPR-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052442.1	1	0	0	19	348	0	62	1	9.998543e-01	2	264	0	62	2			0	0	0	0		1	0.999989	16	343	0	60	2	0	0	0	0	0	0		-3.146461	1	1	0	0		1						0.240000	3.280000									0	0
TACC2	10579	broad.mit.edu	37	10	123976332	123976332	+	Nonsense_Mutation	SNP	C	C	A			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr10:123976332C>A	ENST00000369005.1	+	11	7875	c.7535C>A	c.(7534-7536)tCa>tAa	p.S2512*	TACC2_ENST00000513429.1_Nonsense_Mutation_p.S658*|TACC2_ENST00000515603.1_Nonsense_Mutation_p.S2467*|TACC2_ENST00000368999.1_Nonsense_Mutation_p.S602*|TACC2_ENST00000334433.3_Nonsense_Mutation_p.S2512*|TACC2_ENST00000369001.1_Nonsense_Mutation_p.S216*|TACC2_ENST00000260733.3_Nonsense_Mutation_p.S590*|TACC2_ENST00000369000.1_Nonsense_Mutation_p.S212*|TACC2_ENST00000369004.3_Nonsense_Mutation_p.S602*|TACC2_ENST00000358010.1_Nonsense_Mutation_p.S658*|TACC2_ENST00000453444.2_Nonsense_Mutation_p.S2516*|TACC2_ENST00000515273.1_Nonsense_Mutation_p.S2516*|TACC2_ENST00000360561.3_Nonsense_Mutation_p.S590*	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2			83		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)			AAATTCAGTTCACCCACTGAG	0.562000																								0							SO:0001587	stop_gained			ENST00000369005.1	0	1	hg19	CCDS7626.1	.	.	.	.	.	.	.	.	.	.	C	41	8.660008	0.98903	.	.	ENSG00000138162	ENST00000369005;ENST00000513429;ENST00000515273;ENST00000515603;ENST00000334433;ENST00000358010;ENST00000453444;ENST00000340076;ENST00000369001;ENST00000369000;ENST00000360561;ENST00000368999;ENST00000369004;ENST00000260733;ENST00000514539;ENST00000496913;ENST00000508411	.	.	.	5.64	5.64	0.86602	.	0.000000	0.30356	N	0.009802	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-15.0877	19.7186	0.96134	0.0:1.0:0.0:0.0	.	.	.	.	X	2512;658;2516;2467;2512;658;2516;2502;216;212;590;602;602;590;607;247;92	.	ENSP00000260733:S590X	S	+	2	0	TACC2	123966322	1.000000	0.71417	0.273000	0.24645	0.801000	0.45260	4.972000	0.63756	2.659000	0.90383	0.655000	0.94253	TCA		TCGA-YB-A89D-01A-12D-A36O-08	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1	0	0	0	11	429	0	93	0	3.133931e-01	0	42	0	93	2		0	0	0	0	0	2	1	0.998291	11	425	0	93	2		0	0	0	0	93	2	-3.393814	1	1	0	0		1	1	2	3	1.987911	0	0.240000	3.280000	0.321429	0.230000	0.120000	0.400000	0.240000	0.252176	0.230000	0	1.700000e-01	3.200000e-01
MKI67	4288	broad.mit.edu	37	10	129904176	129904176	+	Silent	SNP	G	G	T			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr10:129904176G>T	ENST00000368654.3	-	13	6303	c.5928C>A	c.(5926-5928)atC>atA	p.I1976I	MKI67_ENST00000368653.3_Silent_p.I1616I	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67			159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)			ATACTTCTGTGATTTTGTCAT	0.473000																								0							SO:0001819	synonymous_variant			ENST00000368654.3	0	1	hg19	CCDS7659.1																																																																																				TCGA-YB-A89D-01A-12D-A36O-08	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	0	0	0	16	1125	0	325	0	1.381052e-02	0	12	0	325	2		0	0	0	0	0	2	1	0.999921	16	1108	0	325	2		0	0	0	0	325	2	-2.297757	0	1	0	0		1	1	2	3	1.958413	0	0.240000	3.280000	0.321429	0.130000	0.070000	0.210000	0.120000	0.138552	0.130000	0	9.000000e-02	1.700000e-01
PFKP	5214	broad.mit.edu	37	10	3149495	3149495	+	Silent	SNP	C	C	A			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr10:3149495C>A	ENST00000381125.4	+	8	940	c.864C>A	c.(862-864)atC>atA	p.I288I	PFKP_ENST00000381075.2_Silent_p.I280I	NM_002627.4	NP_002618.1	Q01813	PFKAP_HUMAN	phosphofructokinase, platelet			31					CTGAGAAAATCAAAGAGGTGA	0.458000																								0							SO:0001819	synonymous_variant			ENST00000381125.4	0	1	hg19	CCDS7059.1																																																																																				TCGA-YB-A89D-01A-12D-A36O-08	PFKP-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046454.1	0	0	0	10	400	0	79	0	9.699477e-01	1	241	0	79	2		0	0	0	0	0	2	1	0.996886	10	398	0	77	2		0	0	0	0	79	2	-9.609288	1	1	0	0		1	1	2	3	1.954405	0	0.240000	3.280000	0.321429	0.230000	0.110000	0.400000	0.240000	0.247906	0.230000	0	1.600000e-01	3.200000e-01
ARHGAP12	94134	broad.mit.edu	37	10	32101656	32101656	+	Missense_Mutation	SNP	G	G	T			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr10:32101656G>T	ENST00000344936.2	-	15	2164	c.1930C>A	c.(1930-1932)Cgt>Agt	p.R644S	ARHGAP12_ENST00000396144.4_Missense_Mutation_p.R639S|ARHGAP12_ENST00000492028.1_5'UTR|ARHGAP12_ENST00000311380.4_Missense_Mutation_p.R592S|ARHGAP12_ENST00000375250.5_Missense_Mutation_p.R614S|ARHGAP12_ENST00000375245.4_Missense_Mutation_p.R592S	NM_001270697.1|NM_018287.6	NP_001257626.1|NP_060757.4	Q8IWW6	RHG12_HUMAN	Rho GTPase activating protein 12			31		Prostate(175;0.0199)			CCTTTTTCACGAACAGCTTGC	0.313000																								0							SO:0001583	missense			ENST00000344936.2	1	0	hg19	CCDS7170.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.569314	0.86439	.	.	ENSG00000165322	ENST00000311380;ENST00000375250;ENST00000344936;ENST00000396144;ENST00000375245	T;T;T;T;T	0.08458	3.15;3.09;3.13;3.12;3.15	5.74	4.79	0.61399	Rho GTPase-activating protein domain (1);	0.000000	0.85682	D	0.000000	T	0.25121	0.0610	M	0.73217	2.22	0.80722	D	1	P;D;D;D;D;D	0.60160	0.906;0.978;0.987;0.978;0.978;0.987	P;P;P;P;P;P	0.61201	0.518;0.77;0.885;0.77;0.77;0.885	T	0.00217	-1.1909	10	0.54805	T	0.06	.	15.5743	0.76362	0.0:0.0:0.8616:0.1384	.	597;614;614;639;644;592	Q1RLN5;B3KR88;Q8IWW6-2;Q504X1;Q8IWW6;Q8IWW6-3	.;.;.;.;RHG12_HUMAN;.	S	592;614;644;639;592	ENSP00000310984:R592S;ENSP00000364399:R614S;ENSP00000345808:R644S;ENSP00000379448:R639S;ENSP00000364394:R592S	ENSP00000310984:R592S	R	-	1	0	ARHGAP12	32141662	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.342000	0.59341	2.703000	0.92315	0.655000	0.94253	CGT		TCGA-YB-A89D-01A-12D-A36O-08	ARHGAP12-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047465.1	1	0	0	20	510	0	75	0	5.002353e-01	0	43	0	75	2		0	0	0	0	0	2	1	0.999995	20	503	0	75	2		0	0	0	0	75	2	-2.874571	1	1	121408	1	33	1	1	2	3	1.954405	0	0.240000	3.280000	0.321429	0.350000	0.220000	0.520000	0.360000	0.366954	0.350000	0	2.800000e-01	4.400000e-01
PGR	5241	broad.mit.edu	37	11	100922228	100922228	+	Missense_Mutation	SNP	C	C	A			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr11:100922228C>A	ENST00000325455.5	-	5	3737	c.2284G>T	c.(2284-2286)Ggt>Tgt	p.G762C	PGR_ENST00000263463.5_Missense_Mutation_p.G660C|PGR_ENST00000534013.1_Missense_Mutation_p.G168C	NM_000926.4|NM_001202474.1|NM_001271162.1	NP_000917.3|NP_001189403.1|NP_001258091.1	P06401	PRGR_HUMAN	progesterone receptor			36		Acute lymphoblastic leukemia(157;0.000885)|all_hematologic(158;0.014)		Allylestrenol(DB01431)|Danazol(DB01406)|Desogestrel(DB00304)|Drospirenone(DB01395)|Dydrogesterone(DB00378)|Ethynodiol(DB00823)|Etonogestrel(DB00294)|Fluticasone Propionate(DB00588)|Levonorgestrel(DB00367)|Medroxyprogesterone Acetate(DB00603)|Megestrol acetate(DB00351)|Mifepristone(DB00834)|Norelgestromin(DB06713)|Norethindrone(DB00717)|Norgestimate(DB00957)|Progesterone(DB00396)|Spironolactone(DB00421)	CATCCTAGACCAAACACCATT	0.348000													Pancreas(124;2271 2354 21954 22882)											0							SO:0001583	missense			ENST00000325455.5	0	1	hg19	CCDS8310.1	.	.	.	.	.	.	.	.	.	.	C	18.40	3.616469	0.66672	.	.	ENSG00000082175	ENST00000325455;ENST00000534013;ENST00000263463;ENST00000537623	D;D;D	0.96619	-4.07;-4.07;-4.07	5.24	5.24	0.73138	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.119765	0.56097	D	0.000031	D	0.98052	0.9358	M	0.77406	2.37	0.27257	N	0.95872	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.85130	0.99;0.997;0.969	D	0.94318	0.7551	10	0.66056	D	0.02	.	18.8379	0.92169	0.0:1.0:0.0:0.0	.	660;762;143	Q8TDS3;P06401;A7LQ08	.;PRGR_HUMAN;.	C	762;168;660;660	ENSP00000325120:G762C;ENSP00000436561:G168C;ENSP00000263463:G660C	ENSP00000263463:G660C	G	-	1	0	PGR	100427438	1.000000	0.71417	1.000000	0.80357	0.847000	0.48162	4.049000	0.57397	2.435000	0.82474	0.650000	0.86243	GGT		TCGA-YB-A89D-01A-12D-A36O-08	PGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394934.1	0	0	0	8	862	0	180	0	1.182257e-04	0	2	0	180	2		0	0	0	0	0	2	1	0.989027	9	854	0	174	2		0	0	0	0	180	2	-2.286708	0	1	0	0		1	1	2	3	1.963000	0	0.240000	3.280000	0.321429	0.080000	0.030000	0.160000	0.090000	0.096135	0.080000	0	5.000000e-02	1.300000e-01
SPTY2D1	144108	broad.mit.edu	37	11	18636809	18636809	+	Nonsense_Mutation	SNP	C	C	A			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr11:18636809C>A	ENST00000336349.5	-	3	1247	c.1012G>T	c.(1012-1014)Gag>Tag	p.E338*	SPTY2D1_ENST00000543776.1_5'Flank	NM_194285.2	NP_919261.2	Q68D10	SPT2_HUMAN	SPT2, Suppressor of Ty, domain containing 1 (S. cerevisiae)			30					GCTTTGTGCTCAACAGCAGAT	0.512000																								0							SO:0001587	stop_gained			ENST00000336349.5	0	1	hg19	CCDS31441.1	.	.	.	.	.	.	.	.	.	.	C	34	5.326405	0.95708	.	.	ENSG00000179119	ENST00000336349	.	.	.	5.84	5.84	0.93424	.	0.272640	0.36815	N	0.002396	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.14252	T	0.57	-18.4727	18.3021	0.90167	0.0:1.0:0.0:0.0	.	.	.	.	X	338	.	ENSP00000337991:E338X	E	-	1	0	SPTY2D1	18593385	1.000000	0.71417	1.000000	0.80357	0.665000	0.39181	2.734000	0.47368	2.762000	0.94881	0.563000	0.77884	GAG		TCGA-YB-A89D-01A-12D-A36O-08	SPTY2D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395941.1	0	0	0	17	807	0	200	0	9.079752e-02	0	23	0	200	2		0	0	0	0	0	2	1	0.999961	15	801	0	200	2		0	0	0	0	200	2	-2.156964	0	1	0	0		1	1	2	3	1.963000	0	0.240000	3.280000	0.321429	0.190000	0.110000	0.300000	0.190000	0.202863	0.190000	0	1.400000e-01	2.500000e-01
ANO3	63982	broad.mit.edu	37	11	26556101	26556101	+	Nonsense_Mutation	SNP	C	C	A			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr11:26556101C>A	ENST00000256737.3	+	9	1820	c.968C>A	c.(967-969)tCa>tAa	p.S323*	ANO3_ENST00000531568.1_Nonsense_Mutation_p.S177*|ANO3_ENST00000537978.1_Nonsense_Mutation_p.S307*|ANO3_ENST00000525139.1_Nonsense_Mutation_p.S307*	NM_031418.2	NP_113606.2	Q9BYT9	ANO3_HUMAN	anoctamin 3			68					AATGGAATATCAAAAGTGGGT	0.318000																								0							SO:0001587	stop_gained			ENST00000256737.3	0	1	hg19	CCDS31447.1	.	.	.	.	.	.	.	.	.	.	C	39	7.882011	0.98542	.	.	ENSG00000134343	ENST00000537978;ENST00000525139;ENST00000256737;ENST00000538001;ENST00000531568	.	.	.	5.03	5.03	0.67393	.	0.390504	0.26959	N	0.021623	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07030	T	0.85	.	17.9596	0.89081	0.0:1.0:0.0:0.0	.	.	.	.	X	307;307;323;225;177	.	ENSP00000256737:S323X	S	+	2	0	ANO3	26512677	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.640000	0.61368	2.349000	0.79799	0.460000	0.39030	TCA		TCGA-YB-A89D-01A-12D-A36O-08	ANO3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387806.1	0	0	0	10	507	0	82		0	0	0	0	82	2		0	0	0	0	0	2	1	0.996811	10	503	0	82	2		0	0	0	0	82	2	-2.794974	1	1	0	0		1	1	2	3	1.963000	0	0.240000	3.280000	0.321429	0.180000	0.090000	0.320000	0.180000	0.197004	0.180000	0	1.300000e-01	2.500000e-01
CTSC	1075	broad.mit.edu	37	11	88029368	88029368	+	Silent	SNP	T	T	C			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08			T	C	T	T		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr11:88029368T>C	ENST00000227266.5	-	6	936	c.822A>G	c.(820-822)ctA>ctG	p.L274L		NM_001814.4	NP_001805	P53634	CATC_HUMAN	cathepsin C			22		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)			AATTGTTGGTTAGTATACGGA	0.448000																								0							SO:0001819	synonymous_variant			ENST00000227266.5	1	1	hg19	CCDS8282.1																																																																																				TCGA-YB-A89D-01A-12D-A36O-08	CTSC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394019.2	1	0	1	47	417	0	108	1	1	33	360	0	108	2		0	0	0	0	0	2	1	1.000000	47	406	0	106	2		0	0	0	0	108	2	-20.000000	1	1	0	0		1	1	2	3	1.963000	0	0.240000	3.280000	0.321429	0.940000	0.700000	1.000000	1.000000	0.922797	0.940000	1	8.200000e-01	1
UNG	7374	broad.mit.edu	37	12	109547720	109547720	+	Silent	SNP	C	C	A			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr12:109547720C>A	ENST00000242576.2	+	7	994	c.888C>A	c.(886-888)acC>acA	p.T296T	RP11-968O1.5_ENST00000541704.2_RNA|UNG_ENST00000336865.2_Silent_p.T287T	NM_080911.2	NP_550433.1			uracil-DNA glycosylase			9					TTTCAAAGACCAATGAGCTGC	0.478000								Base excision repair (BER), DNA glycosylases	Immune Deficiency with Hyper-IgM															0							SO:0001819	synonymous_variant	Familial Cancer Database	Hypogammaglobulinemia with Hyper-IgM, HIGM type I-V, XLHIGM	ENST00000242576.2	0	1	hg19	CCDS9124.1	.	.	.	.	.	.	.	.	.	.	C	10.70	1.423234	0.25639	.	.	ENSG00000076248	ENST00000542183	.	.	.	5.82	4.02	0.46733	.	.	.	.	.	T	0.60340	0.2261	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.61252	-0.7100	5	0.87932	D	0	-14.9663	4.4685	0.11701	0.2511:0.5308:0.0:0.2181	.	.	.	.	Q	50	.	ENSP00000438623:P50Q	P	+	2	0	UNG	108032103	0.609000	0.26975	1.000000	0.80357	0.961000	0.63080	-0.176000	0.09811	0.831000	0.34780	-0.219000	0.12488	CCA		TCGA-YB-A89D-01A-12D-A36O-08	UNG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000403067.1	0	0	0	11	611	0	148	0	2.225271e-01	0	46	0	148	2		0	0	0	0	0	2	1	0.998112	11	597	0	145	2		0	0	0	0	148	2	-2.877963	1	1	121412	1	32	1	1	2	3	1.987213	1	0.240000	3.280000	0.321429	0.160000	0.080000	0.280000	0.160000	0.178873	0.160000	0	1.200000e-01	2.300000e-01
GIT2	9815	broad.mit.edu	37	12	110421488	110421488	+	Silent	SNP	C	C	A	rs140917075		TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr12:110421488C>A	ENST00000355312.3	-	5	416	c.417G>T	c.(415-417)tcG>tcT	p.S139S	GIT2_ENST00000551209.1_Silent_p.S139S|TCHP_ENST00000550780.1_3'UTR|GIT2_ENST00000356259.4_Silent_p.S139S|GIT2_ENST00000338373.5_Silent_p.S139S|GIT2_ENST00000360185.4_Silent_p.S139S|GIT2_ENST00000343646.5_Silent_p.S139S|GIT2_ENST00000354574.4_Silent_p.S139S|GIT2_ENST00000553118.1_Silent_p.S139S|GIT2_ENST00000547815.1_Silent_p.S139S|GIT2_ENST00000320063.9_Silent_p.S139S|GIT2_ENST00000361006.5_Silent_p.S139S|GIT2_ENST00000457474.2_Silent_p.S139S	NM_057169.3	NP_476510.1	Q14161	GIT2_HUMAN	G protein-coupled receptor kinase interacting ArfGAP 2			27					TTCTCACGCTCGAATGGAGTT	0.393000																								0							SO:0001819	synonymous_variant			ENST00000355312.3	1	0	hg19	CCDS9138.1																																																																																				TCGA-YB-A89D-01A-12D-A36O-08	GIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403407.1	1	0	0	19	347	0	78	0	4.983643e-01	0	31	0	78	2		0	0	0	0	0	2	1	0.999991	18	344	0	78	2		0	0	0	0	78	2	-2.745491	1	1	0	0		1	1	2	3	1.987213	1	0.240000	3.280000	0.321429	0.490000	0.300000	0.720000	0.480000	0.504324	0.490000	0	3.800000e-01	6.100000e-01
CCDC63	160762	broad.mit.edu	37	12	111336859	111336859	+	Silent	SNP	C	C	T	rs115748204	by1000genomes	TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr12:111336859C>T	ENST00000308208.5	+	10	1514	c.1272C>T	c.(1270-1272)gaC>gaT	p.D424D	CCDC63_ENST00000545036.1_Silent_p.D384D|CCDC63_ENST00000552694.1_Silent_p.D345D	NM_152591.1	NP_689804.1	Q8NA47	CCD63_HUMAN	coiled-coil domain containing 63			39					TAAACTGTGACGCCACCAAGA	0.498000																								0							SO:0001819	synonymous_variant			ENST00000308208.5	1	1	hg19	CCDS9151.1																																																																																				TCGA-YB-A89D-01A-12D-A36O-08	CCDC63-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404673.2	1	0	1	31	233	0	49		0	0	0	0	49	2		0	0	0	0	0	2	1	1.000000	30	230	0	49	2		0	0	0	0	49	2	-20.000000	1	1	121412	61	46	1	1	2	3	1.987213	1	0.240000	3.280000	0.321429	0.990000	0.770000	1.000000	1.000000	0.971610	0.990000	1	9.200000e-01	1
CAPZA3	93661	broad.mit.edu	37	12	18891447	18891447	+	Missense_Mutation	SNP	G	G	T			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr12:18891447G>T	ENST00000317658.3	+	1	403	c.245G>T	c.(244-246)cGa>cTa	p.R82L	PLCZ1_ENST00000539875.1_5'Flank|PLCZ1_ENST00000435379.1_5'Flank|PLCZ1_ENST00000447925.2_5'Flank|RP11-361I14.2_ENST00000536931.1_RNA|PLCZ1_ENST00000266505.7_5'Flank	NM_033328.2	NP_201585.1	Q96KX2	CAZA3_HUMAN	capping protein (actin filament) muscle Z-line, alpha 3			19	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.0241)	Hepatocellular(102;0.194)			GGCGACTACCGATTTTTTGAC	0.418000																								0							SO:0001583	missense			ENST00000317658.3	1	0	hg19	CCDS8681.1	.	.	.	.	.	.	.	.	.	.	G	14.03	2.413973	0.42817	.	.	ENSG00000177938	ENST00000317658	.	.	.	4.39	4.39	0.52855	.	0.000000	0.64402	D	0.000001	T	0.77725	0.4173	M	0.76727	2.345	0.49051	D	0.999749	D	0.89917	1.0	D	0.85130	0.997	T	0.80856	-0.1195	9	0.87932	D	0	-6.8684	13.8066	0.63236	0.0:0.0:1.0:0.0	.	82	Q96KX2	CAZA3_HUMAN	L	82	.	ENSP00000326238:R82L	R	+	2	0	CAPZA3	18782714	0.886000	0.30341	0.885000	0.34714	0.263000	0.26337	5.868000	0.69605	2.278000	0.76064	0.462000	0.41574	CGA		TCGA-YB-A89D-01A-12D-A36O-08	CAPZA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401902.1	1	0	0	14	387	0	96		0	0	0	0	96	2		0	0	0	0	0	2	1	0.999714	12	378	0	95	2		0	0	0	0	96	2	-2.898136	1	1	0	0		1	1	2	3	1.987213	1	0.240000	3.280000	0.321429	0.330000	0.180000	0.520000	0.330000	0.345567	0.330000	0	2.500000e-01	4.300000e-01
KRAS	3845	broad.mit.edu	37	12	25398284	25398284	+	Missense_Mutation	SNP	C	C	T	rs121913529		TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	KRAS_deep			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	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	0	1	hg19	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.409094	0.83340	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.85919	0.5809	M	0.91818	3.245	0.80722	D	1	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	.	18.3719	0.90409	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	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT		TCGA-YB-A89D-01A-12D-A36O-08	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	0	0	0	6	397	0	85	0	7.864706e-02	0	26	0	85	2	1	8.764639e-01	3	248	0	308	2	1	0.964156	6	393	0	83	2	1	1	175	7854	0	85	2	-3.335946	1	1	121404	2	44	1	1	2	3	1.987213	1	0.240000	3.280000	0.321429	0.140000	0.050000	0.290000	0.150000	0.160471	0.140000	0	9.000000e-02	2.200000e-01
KRAS	3845	broad.mit.edu	37	12	25398285	25398285	+	Missense_Mutation	SNP	C	C	G	rs121913530		TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08			C	G	C	C		Valid	Somatic	Phase_I	WXS	KRAS_deep			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	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	1	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-YB-A89D-01A-12D-A36O-08	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	1	0	1	70	331	1	85	1	8.313397e-01	14	11	1	85	3	1	1	43	209	0	305	2	1	1.000000	70	327	1	83	17	1	1	2046	5983	1	85	210	-20.000000	1	1	0	0		1	1	2	3	1.987213	1	0.240000	3.280000	0.321429	0.990000	0.990000	1.000000	1.000000	0.999999	0.990000	1	9.900000e-01	1
STK38L	23012	broad.mit.edu	37	12	27461299	27461299	+	Missense_Mutation	SNP	C	C	A			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr12:27461299C>A	ENST00000389032.3	+	4	383	c.214C>A	c.(214-216)Cgc>Agc	p.R72S	STK38L_ENST00000539577.1_Intron	NM_015000.3	NP_055815.1			serine/threonine kinase 38 like			12	Colorectal(261;0.0847)				ACAACACGCTCGCAAAGAAAC	0.368000																								0							SO:0001583	missense			ENST00000389032.3	1	0	hg19	CCDS31761.1	.	.	.	.	.	.	.	.	.	.	C	17.50	3.405421	0.62288	.	.	ENSG00000211455	ENST00000541191;ENST00000389032;ENST00000540996;ENST00000543246;ENST00000544969	T;T;T;T;T	0.49720	0.99;0.77;0.99;0.99;0.99	4.54	4.54	0.55810	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.46639	0.1403	L	0.56199	1.76	0.80722	D	1	B	0.10296	0.003	B	0.12837	0.008	T	0.46331	-0.9199	10	0.51188	T	0.08	.	17.29	0.87153	0.0:1.0:0.0:0.0	.	72	Q9Y2H1	ST38L_HUMAN	S	72	ENSP00000437856:R72S;ENSP00000373684:R72S;ENSP00000443838:R72S;ENSP00000442253:R72S;ENSP00000440279:R72S	ENSP00000373684:R72S	R	+	1	0	STK38L	27352566	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.515000	0.60489	2.257000	0.74773	0.460000	0.39030	CGC		TCGA-YB-A89D-01A-12D-A36O-08	STK38L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403297.1	1	0	0	35	678	0	132	0	8.695156e-01	0	72	0	132	2		0	0	0	0	0	2	1	1.000000	35	665	0	130	2		0	0	0	0	132	2	-2.489183	0	1	0	0		1	1	2	3	1.987213	1	0.240000	3.280000	0.321429	0.450000	0.320000	0.620000	0.450000	0.468540	0.450000	0	3.800000e-01	5.400000e-01
RPAP3	79657	broad.mit.edu	37	12	48095372	48095372	+	Silent	SNP	G	G	T			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr12:48095372G>T	ENST00000005386.3	-	3	284	c.169C>A	c.(169-171)Cga>Aga	p.R57R	RPAP3_ENST00000380650.4_Silent_p.R57R|RPAP3_ENST00000432584.3_5'UTR	NM_024604.2	NP_078880.2	Q9H6T3	RPAP3_HUMAN	RNA polymerase II associated protein 3			16	Lung SC(27;0.192)				TTCCCATTTCGAATAGGAGGT	0.308000																								0							SO:0001819	synonymous_variant			ENST00000005386.3	1	0	hg19	CCDS8753.1																																																																																				TCGA-YB-A89D-01A-12D-A36O-08	RPAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405340.1	1	0	0	12	339	0	42	0	1.818985e-01	0	21	0	42	2		0	0	0	0	0	2	1	0.999044	12	331	0	40	2		0	0	0	0	42	2	-3.502636	1	1	0	0		1	1	2	3	1.987213	1	0.240000	3.280000	0.321429	0.320000	0.170000	0.530000	0.330000	0.341656	0.320000	0	2.400000e-01	4.300000e-01
RAP1B	5908	broad.mit.edu	37	12	69050210	69050210	+	Nonsense_Mutation	SNP	C	C	A			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr12:69050210C>A	ENST00000250559.9	+	6	680	c.449C>A	c.(448-450)tCa>tAa	p.S150*	RAP1B_ENST00000341355.5_Nonsense_Mutation_p.S150*|RAP1B_ENST00000539091.1_Nonsense_Mutation_p.S108*|RAP1B_ENST00000378985.3_Nonsense_Mutation_p.S84*|RAP1B_ENST00000393436.5_Nonsense_Mutation_p.S150*|RAP1B_ENST00000541216.1_Nonsense_Mutation_p.S150*|RAP1B_ENST00000537460.1_Nonsense_Mutation_p.S150*|RAP1B_ENST00000450214.2_Nonsense_Mutation_p.S108*|RAP1B_ENST00000463493.1_3'UTR|RAP1B_ENST00000543697.1_Intron|RAP1B_ENST00000542145.1_Nonsense_Mutation_p.S103*|RAP1B_ENST00000540209.1_Nonsense_Mutation_p.S131*|RAP1B_ENST00000543393.1_Nonsense_Mutation_p.S84*	NM_001010942.2|NM_001251921.1|NM_001251922.1|NM_015646.5	NP_001010942.1|NP_001238850.1|NP_001238851.1|NP_056461.1	P61224	RAP1B_HUMAN	RAP1B, member of RAS oncogene family			12	Breast(13;1.24e-05)		Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.00694)		TCTGCAAAATCAAAAATAAAT	0.338000																								0							SO:0001587	stop_gained			ENST00000250559.9	0	1	hg19	CCDS8984.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.817521	0.90790	.	.	ENSG00000127314	ENST00000250559;ENST00000393436;ENST00000425247;ENST00000341355;ENST00000537460;ENST00000450214;ENST00000538980;ENST00000543393;ENST00000378985;ENST00000540209;ENST00000535492;ENST00000539091;ENST00000542145;ENST00000541216	.	.	.	5.6	5.6	0.85130	.	0.136637	0.48767	D	0.000161	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.9958	0.97383	0.0:1.0:0.0:0.0	.	.	.	.	X	150;150;150;150;150;108;99;84;84;131;84;108;103;150	.	.	S	+	2	0	RAP1B	67336477	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.532000	0.60608	2.802000	0.96397	0.561000	0.74099	TCA		TCGA-YB-A89D-01A-12D-A36O-08	RAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257821.3	0	0	0	15	507	0	119	0	8.537126e-01	0	119	0	119	2		0	0	0	0	0	2	1	0.999859	15	499	0	140	2		0	0	0	0	119	2	-2.940284	1	1	0	0		1	1	2	3	1.987213	1	0.240000	3.280000	0.321429	0.270000	0.150000	0.420000	0.270000	0.283833	0.270000	0	2.000000e-01	3.500000e-01
CPSF6	11052	broad.mit.edu	37	12	69646912	69646912	+	Silent	SNP	C	C	A			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr12:69646912C>A	ENST00000435070.2	+	3	462	c.352C>A	c.(352-354)Cgg>Agg	p.R118R	CPSF6_ENST00000456847.3_Silent_p.R118R|CPSF6_ENST00000266679.8_Silent_p.R118R|CPSF6_ENST00000550987.1_3'UTR|CPSF6_ENST00000551516.1_Intron	NM_007007.2	NP_008938.2	Q16630	CPSF6_HUMAN	cleavage and polyadenylation specific factor 6, 68kDa			16	all_epithelial(5;2.47e-36)|Lung NSC(4;1.1e-32)|all_lung(4;6.26e-31)|Breast(13;1.59e-06)|Esophageal squamous(21;0.187)		Epithelial(6;4.89e-17)|BRCA - Breast invasive adenocarcinoma(5;8.5e-10)|Lung(24;6.04e-05)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.0151)|LUSC - Lung squamous cell carcinoma(43;0.171)|Kidney(9;0.241)		TTTTGAAAATCGGGCAAATGG	0.323000																								0							SO:0001819	synonymous_variant			ENST00000435070.2	1	0	hg19	CCDS8988.1																																																																																				TCGA-YB-A89D-01A-12D-A36O-08	CPSF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403609.1	1	0	0	14	286	0	60	0	6.597680e-01	0	47	0	60	2		0	0	0	0	0	2	1	0.999778	14	287	0	60	2		0	0	0	0	60	2	-4.415923	1	1	0	0		1	1	2	3	1.987213	1	0.240000	3.280000	0.321429	0.440000	0.250000	0.690000	0.430000	0.460319	0.440000	0	3.300000e-01	5.700000e-01
FRY	10129	broad.mit.edu	37	13	32747655	32747655	+	Missense_Mutation	SNP	G	G	T			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr13:32747655G>T	ENST00000380250.3	+	19	2799	c.2303G>T	c.(2302-2304)cGa>cTa	p.R768L		NM_023037.2	NP_075463.2	Q5TBA9	FRY_HUMAN	furry homolog (Drosophila)			132		Lung SC(185;0.0271)			AAGGAAATTCGAGCGTTGTTT	0.413000																								0							SO:0001583	missense			ENST00000380250.3	1	0	hg19	CCDS41875.1	.	.	.	.	.	.	.	.	.	.	G	27.1	4.795934	0.90453	.	.	ENSG00000073910	ENST00000380250	T	0.27720	1.65	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	T	0.59074	0.2167	M	0.74881	2.28	0.80722	D	1	D	0.76494	0.999	D	0.77557	0.99	T	0.59579	-0.7428	10	0.62326	D	0.03	.	19.9564	0.97221	0.0:0.0:1.0:0.0	.	768	Q5TBA9	FRY_HUMAN	L	768	ENSP00000369600:R768L	ENSP00000369600:R768L	R	+	2	0	FRY	31645655	1.000000	0.71417	0.999000	0.59377	0.651000	0.38670	9.402000	0.97298	2.708000	0.92522	0.650000	0.86243	CGA		TCGA-YB-A89D-01A-12D-A36O-08	FRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044405.1	1	0	0	22	568	0	113	0	3.719397e-02	0	8	0	113	2		0	0	0	0	0	2	1	0.999999	20	562	0	112	2		0	0	0	0	113	2	-3.030118	1	1	0	0		1	2	2	4	2.158430	1	0.240000	3.280000	0.387097	0.380000	0.240000	0.560000	0.400000	0.400396	0.380000	0	3.100000e-01	4.800000e-01
SUCLA2	8803	broad.mit.edu	37	13	48570988	48570988	+	Silent	SNP	G	G	T			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr13:48570988G>T	ENST00000378654.3	-	2	317	c.261C>A	c.(259-261)gcC>gcA	p.A87A	SUCLA2_ENST00000543413.1_Silent_p.A29A|SUCLA2_ENST00000497202.1_5'UTR|SUCLA2_ENST00000544100.1_5'UTR|SUCLA2_ENST00000534875.1_Silent_p.A29A	NM_003850.2	NP_003841.1	Q9P2R7	SUCB1_HUMAN	succinate-CoA ligase, ADP-forming, beta subunit			15		all_cancers(8;1.13e-24)|all_epithelial(8;1.78e-13)|all_lung(13;2.85e-06)|Breast(56;0.000141)|Lung NSC(96;0.000226)|all_hematologic(8;0.000885)|Prostate(109;0.00132)|Acute lymphoblastic leukemia(8;0.0167)|Myeloproliferative disorder(33;0.039)|Hepatocellular(98;0.0556)|Lung SC(185;0.102)|Glioma(44;0.236)		Succinic acid(DB00139)	CTAATTTTTTGGCAATTGCAT	0.368000																								0							SO:0001819	synonymous_variant			ENST00000378654.3	0	1	hg19	CCDS9406.1																																																																																				TCGA-YB-A89D-01A-12D-A36O-08	SUCLA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044852.1	0	0	0	9	600	0	104	0	2.051197e-01	0	51	0	104	2		0	0	0	0	0	2	1	0.994097	9	596	0	103	2		0	0	0	0	104	2	-3.022994	1	1	0	0		1	2	2	4	2.158430	1	0.240000	3.280000	0.387097	0.150000	0.060000	0.280000	0.160000	0.168680	0.150000	0	1.000000e-01	2.200000e-01
DDHD1	80821	broad.mit.edu	37	14	53518604	53518604	+	Missense_Mutation	SNP	G	G	T			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr14:53518604G>T	ENST00000323669.5	-	12	2478	c.2479C>A	c.(2479-2481)Ctt>Att	p.L827I	DDHD1_ENST00000395606.1_Intron|DDHD1_ENST00000357758.3_Intron|DDHD1_ENST00000555621.1_Intron	NM_001160148.1	NP_001153620.1	Q8NEL9	DDHD1_HUMAN	DDHD domain containing 1			25	Breast(41;0.037)				TCCGGAAAAAGAAGTTGTGGG	0.343000																								0							SO:0001583	missense			ENST00000323669.5	1	1	hg19	CCDS53895.1	.	.	.	.	.	.	.	.	.	.	G	16.48	3.135008	0.56828	.	.	ENSG00000100523	ENST00000323669;ENST00000395610	.	.	.	6.07	5.19	0.71726	DDHD (2);	0.301493	0.30969	N	0.008510	T	0.36413	0.0966	N	0.08118	0	0.80722	D	1	P	0.38048	0.616	B	0.42738	0.396	T	0.28138	-1.0053	9	0.31617	T	0.26	-10.4012	11.0964	0.48147	0.084:0.0:0.916:0.0	.	827	Q8NEL9	DDHD1_HUMAN	I	827;698	.	ENSP00000327104:L827I	L	-	1	0	DDHD1	52588354	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.931000	0.48932	1.582000	0.49881	0.655000	0.94253	CTT		TCGA-YB-A89D-01A-12D-A36O-08	DDHD1-003	KNOWN	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276901.1	1	0	1	18	58	0	19	0	6.697109e-01	1	8	0	19	2		0	0	0	0	0	2	1	0.999991	17	57	0	19	2		0	0	0	0	19	2	-20.000000	1	1	119994	1	24	1	2	2	4	2.116095	1	0.240000	3.280000	0.378679	0.990000	0.990000	1.000000	1.000000	0.999989	0.990000	1	9.900000e-01	1
LTBP2	4053	broad.mit.edu	37	14	75052666	75052666	+	Nonsense_Mutation	SNP	C	C	A			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08			C	A	C	C		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr14:75052666C>A	ENST00000261978.4	-	3	1107	c.721G>T	c.(721-723)Gag>Tag	p.E241*	LTBP2_ENST00000557425.1_Intron|LTBP2_ENST00000556690.1_Nonsense_Mutation_p.E241*	NM_000428.2	NP_000419.1	Q14767	LTBP2_HUMAN	latent transforming growth factor beta binding protein 2			58					GGTGAACGCTCGGCCCAGCGT	0.672000																								0							SO:0001587	stop_gained			ENST00000261978.4	0	0	hg19	CCDS9831.1	.	.	.	.	.	.	.	.	.	.	C	37	6.538623	0.97646	.	.	ENSG00000119681	ENST00000261978;ENST00000556690	.	.	.	5.41	2.53	0.30540	.	0.196421	0.25750	N	0.028553	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.074	0.48021	0.1337:0.4776:0.3887:0.0	.	.	.	.	X	241	.	ENSP00000261978:E241X	E	-	1	0	LTBP2	74122419	0.000000	0.05858	0.008000	0.14137	0.056000	0.15407	0.464000	0.21988	0.237000	0.21200	-0.302000	0.09304	GAG		TCGA-YB-A89D-01A-12D-A36O-08	LTBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413595.1	1	0	1	10	102	0	18	0	9.995907e-01	0	155	0	18	2		0	0	0	0	0	2	1	0.996910	9	100	0	18	2		0	0	0	0	18	2	-15.538530	1	1	0	0		1	2	2	4	2.116095	1	0.240000	3.280000	0.378679	0.960000	0.490000	1.000000	1.000000	0.880017	0.960000	1	6.900000e-01	1
BTBD7	55727	broad.mit.edu	37	14	93761126	93761126	+	Silent	SNP	G	G	T	rs146080654		TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr14:93761126G>T	ENST00000334746.5	-	3	547	c.240C>A	c.(238-240)gcC>gcA	p.A80A	BTBD7_ENST00000554565.1_Intron|BTBD7_ENST00000555525.1_Silent_p.A80A|BTBD7_ENST00000298896.3_Silent_p.A80A|BTBD7_ENST00000393170.2_5'Flank	NM_001002860.2	NP_001002860.2	Q9P203	BTBD7_HUMAN	BTB (POZ) domain containing 7			35		all_cancers(154;0.08)			TGGCATGATCGGCAGACCTAT	0.448000																								0							SO:0001819	synonymous_variant			ENST00000334746.5	0	1	hg19	CCDS32146.1																																																																																				TCGA-YB-A89D-01A-12D-A36O-08	BTBD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412701.1	0	0	0	14	1003	0	243	0	2.295539e-04	0	2	0	243	2		0	0	0	0	0	2	1	0.999713	10	988	0	243	2		0	0	0	0	243	2	-1.827653	0	1	0	0		1	2	2	4	2.116702	1	0.240000	3.280000	0.378679	0.140000	0.070000	1.000000	0.150000	0.197215	0.140000	0	1.000000e-01	2.000000e-01
ATP10A	57194	broad.mit.edu	37	15	25928570	25928570	+	Missense_Mutation	SNP	C	C	G			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr15:25928570C>G	ENST00000356865.6	-	17	3466	c.3355G>C	c.(3355-3357)Gac>Cac	p.D1119H		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A			103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)			TACCACTGGTCAATCATGGTA	0.502000																								0							SO:0001583	missense			ENST00000356865.6	0	1	hg19	CCDS32178.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.693762	0.88735	.	.	ENSG00000206190	ENST00000356865	T	0.42131	0.98	4.81	4.81	0.61882	.	0.000000	0.85682	D	0.000000	T	0.74861	0.3772	H	0.94658	3.565	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.83740	0.0203	10	0.87932	D	0	-36.8332	17.8828	0.88845	0.0:1.0:0.0:0.0	.	1119	O60312	AT10A_HUMAN	H	1119	ENSP00000349325:D1119H	ENSP00000349325:D1119H	D	-	1	0	ATP10A	23479663	1.000000	0.71417	0.998000	0.56505	0.974000	0.67602	7.511000	0.81718	2.205000	0.71048	0.655000	0.94253	GAC		TCGA-YB-A89D-01A-12D-A36O-08	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	0	0	0	5	202	0	27	0	9.840360e-02	0	18	0	27	2		0	0	0	0	0	2	1	0.935072	2	201	0	25	2		0	0	0	0	27	2	-6.952168	1	0	0	0		1	2	2	4	2.075635	0	0.240000	3.280000	0.367510	0.280000	0.100000	1.000000	0.250000	0.374983	0.280000	0	1.700000e-01	5.200000e-01
ARHGAP11A	9824	broad.mit.edu	37	15	32928050	32928050	+	Silent	SNP	C	C	A			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr15:32928050C>A	ENST00000361627.3	+	11	2139	c.1417C>A	c.(1417-1419)Cga>Aga	p.R473R	ARHGAP11A_ENST00000567348.1_Silent_p.R473R|ARHGAP11A_ENST00000543522.1_Silent_p.R284R|ARHGAP11A_ENST00000565905.1_Silent_p.R284R|ARHGAP11A_ENST00000563864.1_Silent_p.R445R	NM_014783.3	NP_055598.1	Q6P4F7	RHGBA_HUMAN	Rho GTPase activating protein 11A	p.R473*(1)		31		all_lung(180;1.3e-11)			TTTAAAAAATCGAATTGAATC	0.313000													Colon(45;757 1134 30003 36652)											1	Substitution - Nonsense(1)						SO:0001819	synonymous_variant			ENST00000361627.3	1	0	hg19	CCDS10028.1																																																																																				TCGA-YB-A89D-01A-12D-A36O-08	ARHGAP11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251417.1	1	0	0	20	340	0	55	0	9.429507e-02	0	9	0	55	2		0	0	0	0	0	2	1	0.999995	20	337	0	55	2		0	0	0	0	55	2	-5.485584	1	0	0	0		1	2	2	4	2.075635	0	0.240000	3.280000	0.367510	0.580000	0.360000	1.000000	0.560000	0.631092	0.580000	0	4.600000e-01	8.100000e-01
HEXA	3073	broad.mit.edu	37	15	72643552	72643552	+	Missense_Mutation	SNP	C	C	A			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr15:72643552C>A	ENST00000268097.5	-	6	1097	c.594G>T	c.(592-594)ttG>ttT	p.L198F	HEXA_ENST00000457859.2_Missense_Mutation_p.L6F|HEXA_ENST00000566304.1_Missense_Mutation_p.L209F|HEXA_ENST00000429918.2_Missense_Mutation_p.L25F|HEXA_ENST00000567159.1_Missense_Mutation_p.L198F|RP11-106M3.3_ENST00000570175.1_RNA|RP11-106M3.2_ENST00000379915.4_RNA	NM_000520.4	NP_000511.2	P06865	HEXA_HUMAN	hexosaminidase A (alpha polypeptide)			24					GGAACACGTTCAATTTATTGT	0.473000																								0							SO:0001583	missense			ENST00000268097.5	0	1	hg19	CCDS10243.1	.	.	.	.	.	.	.	.	.	.	C	15.18	2.755942	0.49362	.	.	ENSG00000213614	ENST00000268097;ENST00000457859;ENST00000429918	D;D;D	0.96913	-4.17;-4.17;-4.17	5.78	3.88	0.44766	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);Glycoside hydrolase, family 20, catalytic core (1);Glycoside hydrolase, family 20 (1);	0.228413	0.45361	N	0.000368	D	0.86752	0.6008	N	0.04669	-0.19	0.38384	D	0.945222	B;B;B;B;B	0.15719	0.014;0.001;0.014;0.006;0.002	B;B;B;B;B	0.22152	0.038;0.019;0.038;0.023;0.018	T	0.77789	-0.2456	10	0.07482	T	0.82	-10.1601	5.9301	0.19134	0.0715:0.2888:0.5184:0.1213	.	25;209;25;78;198	E9PGL4;B4DVA7;B4DVL8;Q9BVJ8;P06865	.;.;.;.;HEXA_HUMAN	F	198;6;25	ENSP00000268097:L198F;ENSP00000398026:L6F;ENSP00000416187:L25F	ENSP00000268097:L198F	L	-	3	2	HEXA	70430606	0.986000	0.35501	1.000000	0.80357	0.993000	0.82548	0.207000	0.17395	0.750000	0.32877	0.655000	0.94253	TTG		TCGA-YB-A89D-01A-12D-A36O-08	HEXA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257317.2	0	0	0	9	348	0	64	0	9.376395e-01	0	189	0	64	2		0	0	0	0	0	2	1	0.994065	9	344	0	63	2		0	0	0	0	64	2	-3.754876	1	1	0	0		1	2	2	4	2.131181	1	0.240000	3.280000	0.384715	0.270000	0.120000	0.510000	0.260000	0.292441	0.270000	0	1.900000e-01	3.800000e-01
ORAI3	93129	broad.mit.edu	37	16	30960680	30960680	+	Missense_Mutation	SNP	T	T	G			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr16:30960680T>G	ENST00000318663.4	+	1	294	c.70T>G	c.(70-72)Tcg>Gcg	p.S24A	ORAI3_ENST00000562699.1_Missense_Mutation_p.S24A|ORAI3_ENST00000566237.1_Missense_Mutation_p.S24A|AC135048.13_ENST00000566056.1_RNA	NM_152288.2	NP_689501.1	Q9BRQ5	ORAI3_HUMAN	ORAI calcium release-activated calcium modulator 3			6					CCCTGCAGGCTCGGCCACGTA	0.736000																								0							SO:0001583	missense			ENST00000318663.4	0	1	hg19	CCDS10697.1	.	.	.	.	.	.	.	.	.	.	T	13.94	2.385910	0.42308	.	.	ENSG00000175938	ENST00000318663;ENST00000420438	T	0.30981	1.51	5.34	4.22	0.49857	.	0.000000	0.43416	D	0.000562	T	0.15609	0.0376	N	0.19112	0.55	0.29807	N	0.831965	B	0.16603	0.018	B	0.16722	0.016	T	0.24404	-1.0161	10	0.10902	T	0.67	-5.3366	5.6272	0.17488	0.1518:0.0818:0.0:0.7664	.	24	Q9BRQ5	ORAI3_HUMAN	A	24	ENSP00000322249:S24A	ENSP00000322249:S24A	S	+	1	0	ORAI3	30868181	0.003000	0.15002	0.999000	0.59377	0.858000	0.48976	0.638000	0.24674	0.816000	0.34421	0.402000	0.26972	TCG		TCGA-YB-A89D-01A-12D-A36O-08	ORAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255545.20	0	0	0	7	18	0	9	1	9.776433e-01	8	14	0	9	2		0	0	0	0	0	2	1	0.983788	6	18	0	8	2		0	0	0	0	9	2	-19.813890	1	1	0	0		1	2	2	4	2.140938	1	0.240000	3.280000	0.387097	0.990000	0.990000	1.000000	1.000000	0.999501	0.990000	1	9.900000e-01	1
ABCC12	94160	broad.mit.edu	37	16	48149365	48149365	+	Silent	SNP	G	G	T			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr16:48149365G>T	ENST00000311303.3	-	13	2295	c.1950C>A	c.(1948-1950)ctC>ctA	p.L650L	ABCC12_ENST00000448542.1_Silent_p.L650L|ABCC12_ENST00000416054.1_Nonsense_Mutation_p.S626*	NM_033226.2	NP_150229.2	Q96J65	MRP9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 12			90		all_cancers(37;0.0474)|all_lung(18;0.047)			TCTTTCCCCTGAGCGTCTTCT	0.607000																								0							SO:0001819	synonymous_variant			ENST00000311303.3	0	1	hg19	CCDS10730.1	.	.	.	.	.	.	.	.	.	.	G	36	5.711257	0.96821	.	.	ENSG00000140798	ENST00000416054	.	.	.	5.24	0.714	0.18180	.	.	.	.	.	.	.	.	.	.	.	0.47123	A	0.999322	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	1.794	0.03057	0.2309:0.2487:0.3932:0.1272	.	.	.	.	X	626	.	ENSP00000413046:S626X	S	-	2	0	ABCC12	46706866	0.000000	0.05858	0.903000	0.35520	0.535000	0.34838	-0.463000	0.06696	0.286000	0.22352	0.467000	0.42956	TCA		TCGA-YB-A89D-01A-12D-A36O-08	ABCC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256837.1	0	0	0	12	696	0	149		0	0	0	0	149	2		0	0	0	0	0	2	1	0.999057	11	689	0	147	2		0	0	0	0	149	2	-2.437183	0	1	0	0		1	2	2	4	2.140938	1	0.240000	3.280000	0.387097	0.170000	0.090000	0.300000	0.170000	0.188784	0.170000	0	1.300000e-01	2.400000e-01
CCDC135	0	broad.mit.edu	37	16	57765164	57765164	+	Missense_Mutation	SNP	C	C	A	rs147283561		TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr16:57765164C>A	ENST00000360716.3	+	19	2840	c.2619C>A	c.(2617-2619)ttC>ttA	p.F873L	CCDC135_ENST00000336825.8_Missense_Mutation_p.F808L|CCDC135_ENST00000394337.4_Missense_Mutation_p.F873L			Q8IY82	CC135_HUMAN				30					AGAAAATATTCGCTTGATGTC	0.567000																								0							SO:0001583	missense			ENST00000360716.3	1	0	hg19	CCDS10787.1	.	.	.	.	.	.	.	.	.	.	c	12.41	1.930949	0.34096	.	.	ENSG00000159625	ENST00000394337;ENST00000336825;ENST00000360716	T;T;T	0.09723	3.1;2.95;3.1	5.06	-0.957	0.10350	.	0.227351	0.36665	N	0.002467	T	0.08626	0.0214	L	0.41236	1.265	0.09310	N	1	B;B	0.20988	0.05;0.05	B;B	0.20577	0.03;0.03	T	0.21793	-1.0235	10	0.87932	D	0	-3.8298	8.998	0.36063	0.0:0.5145:0.0:0.4855	.	808;873	Q8IY82-2;Q8IY82	.;CC135_HUMAN	L	873;808;873	ENSP00000377869:F873L;ENSP00000338938:F808L;ENSP00000353942:F873L	ENSP00000338938:F808L	F	+	3	2	CCDC135	56322665	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.195000	0.03043	-0.511000	0.06514	-0.503000	0.04515	TTC		TCGA-YB-A89D-01A-12D-A36O-08	CCDC135-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433323.2	1	0	0	10	258	0	43	0	0	0	1	0	43	2		0	0	0	0	0	2	1	0.996797	10	254	0	42	2		0	0	0	0	43	2	-11.236540	1	1	0	0		1	2	2	4	2.150367	1	0.240000	3.280000	0.387097	0.400000	0.200000	0.670000	0.390000	0.418509	0.400000	0	2.900000e-01	5.400000e-01
NAE1	8883	broad.mit.edu	37	16	66842917	66842917	+	Missense_Mutation	SNP	C	C	A			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr16:66842917C>A	ENST00000290810.3	-	16	1309	c.1212G>T	c.(1210-1212)ttG>ttT	p.L404F	NAE1_ENST00000394074.2_Missense_Mutation_p.L315F|NAE1_ENST00000359087.4_Missense_Mutation_p.L407F|NAE1_ENST00000379463.2_Missense_Mutation_p.L398F			Q13564	ULA1_HUMAN	NEDD8 activating enzyme E1 subunit 1			18		Ovarian(137;0.0563)		Adenosine triphosphate(DB00171)	TAATTGTATCCAAACCATATT	0.308000																								0							SO:0001583	missense			ENST00000290810.3	0	1	hg19	CCDS10820.1	.	.	.	.	.	.	.	.	.	.	C	11.82	1.753914	0.31046	.	.	ENSG00000159593	ENST00000359087;ENST00000290810;ENST00000379463;ENST00000394074	T;T;T;T	0.46819	0.86;0.86;0.86;0.86	5.14	3.2	0.36748	Molybdenum cofactor biosynthesis, MoeB (1);NAD(P)-binding domain (1);	0.074073	0.56097	D	0.000034	T	0.31482	0.0798	N	0.25647	0.755	0.48975	D	0.999734	B;B;B	0.25609	0.002;0.065;0.13	B;B;B	0.23716	0.004;0.041;0.048	T	0.13791	-1.0496	10	0.51188	T	0.08	-11.51	7.5134	0.27587	0.0:0.7108:0.0:0.2892	.	407;404;398	A6NCK0;Q13564;A6NFN4	.;ULA1_HUMAN;.	F	407;404;398;315	ENSP00000351990:L407F;ENSP00000290810:L404F;ENSP00000368776:L398F;ENSP00000377637:L315F	ENSP00000290810:L404F	L	-	3	2	NAE1	65400418	0.997000	0.39634	0.983000	0.44433	0.906000	0.53458	0.839000	0.27586	1.167000	0.42706	0.650000	0.86243	TTG		TCGA-YB-A89D-01A-12D-A36O-08	NAE1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000268832.1	0	0	0	8	557	0	60	0	5.752158e-01	0	128	0	60	2		0	0	0	0	0	2	1	0.989062	8	552	0	59	2		0	0	0	0	60	2	-3.143328	1	1	0	0		1	2	2	4	2.150367	1	0.240000	3.280000	0.387097	0.150000	0.060000	0.280000	0.160000	0.163568	0.150000	0	1.000000e-01	2.200000e-01
NFATC3	4775	broad.mit.edu	37	16	68208395	68208395	+	Silent	SNP	C	C	A			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr16:68208395C>A	ENST00000346183.3	+	6	1917	c.1893C>A	c.(1891-1893)atC>atA	p.I631I	NFATC3_ENST00000535127.2_3'UTR|NFATC3_ENST00000329524.4_Silent_p.I631I|NFATC3_ENST00000349223.5_Silent_p.I631I|NFATC3_ENST00000575270.1_Silent_p.I631I	NM_173165.2	NP_775188.1	Q12968	NFAC3_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 3			44		Ovarian(137;0.0563)			AATCCAAAATCATTTTTCTTG	0.318000																								0							SO:0001819	synonymous_variant			ENST00000346183.3	0	1	hg19	CCDS10860.1																																																																																				TCGA-YB-A89D-01A-12D-A36O-08	NFATC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268890.2	0	0	0	15	826	0	160	0	9.785164e-03	0	8	0	160	2		0	0	0	0	0	2	1	0.999855	15	815	0	156	2		0	0	0	0	160	2	-2.567233	1	1	0	0		1	2	2	4	2.150367	1	0.240000	3.280000	0.387097	0.180000	0.090000	0.300000	0.200000	0.195760	0.180000	0	1.400000e-01	2.400000e-01
MLKL	197259	broad.mit.edu	37	16	74719433	74719433	+	Missense_Mutation	SNP	G	G	T			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr16:74719433G>T	ENST00000308807.7	-	5	1234	c.771C>A	c.(769-771)ttC>ttA	p.F257L	MLKL_ENST00000306247.7_Intron	NM_152649.2	NP_689862.1			mixed lineage kinase domain-like			19					TGGGAGATTCGAATTTCTTCA	0.398000																								0							SO:0001583	missense			ENST00000308807.7	1	0	hg19	CCDS32487.1	.	.	.	.	.	.	.	.	.	.	G	7.777	0.708709	0.15239	.	.	ENSG00000168404	ENST00000308807	D	0.90676	-2.71	4.58	0.971	0.19698	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.053881	0.85682	D	0.000000	D	0.82360	0.5020	N	0.16307	0.4	0.31299	N	0.688554	P	0.35456	0.502	P	0.45577	0.486	T	0.75436	-0.3318	10	0.09843	T	0.71	-14.296	6.3918	0.21591	0.6871:0.0:0.3129:0.0	.	257	Q8NB16	MLKL_HUMAN	L	257	ENSP00000308351:F257L	ENSP00000308351:F257L	F	-	3	2	MLKL	73276934	1.000000	0.71417	1.000000	0.80357	0.097000	0.18754	1.637000	0.37155	0.287000	0.22375	-0.355000	0.07637	TTC		TCGA-YB-A89D-01A-12D-A36O-08	MLKL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436403.3	1	0	0	18	389	0	78	0	6.089327e-01	0	45	0	78	2		0	0	0	0	0	2	1	0.999981	18	385	0	76	2		0	0	0	0	78	2	-4.604542	1	1	121410	1	40	1	2	2	4	2.150367	1	0.240000	3.280000	0.387097	0.460000	0.280000	0.690000	0.450000	0.478177	0.460000	0	3.600000e-01	5.800000e-01
CNTNAP1	8506	broad.mit.edu	37	17	40837398	40837398	+	Silent	SNP	C	C	A			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr17:40837398C>A	ENST00000264638.4	+	5	892	c.675C>A	c.(673-675)ctC>ctA	p.L225L	CCR10_ENST00000591765.1_5'Flank|CTD-3193K9.3_ENST00000592440.1_RNA	NM_003632.2	NP_003623.1	P78357	CNTP1_HUMAN	contactin associated protein 1			49		Breast(137;0.000143)			ACGTGACGCTCGAGCTGGAGG	0.662000																								0							SO:0001819	synonymous_variant			ENST00000264638.4	1	0	hg19	CCDS11436.1																																																																																				TCGA-YB-A89D-01A-12D-A36O-08	CNTNAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452342.1	1	0	0	13	185	0	49	0	1.291590e-01	1	8	0	49	2		0	0	0	0	0	2	1	0.999529	13	181	0	46	2		0	0	0	0	49	2	-16.812820	1	0	0	0		1	2	2	4	2.138905	1	0.240000	3.280000	0.385908	0.690000	0.390000	1.000000	1.000000	0.708502	0.690000	0	5.200000e-01	9.000000e-01
TRIM25	7706	broad.mit.edu	37	17	54972919	54972919	+	Silent	SNP	C	C	A	rs145816750	by1000genomes	TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr17:54972919C>A	ENST00000316881.4	-	7	1276	c.1227G>T	c.(1225-1227)ccG>ccT	p.P409P	TRIM25_ENST00000537230.1_Silent_p.P409P	NM_005082.4	NP_005073.2	Q14258	TRI25_HUMAN	tripartite motif containing 25			21	Breast(9;6.15e-08)				CTAACTGTTCCGGGGCTCCAA	0.517000																								0							SO:0001819	synonymous_variant			ENST00000316881.4	0	1	hg19	CCDS11591.1																																																																																				TCGA-YB-A89D-01A-12D-A36O-08	TRIM25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440609.1	0	0	0	11	699	0	142	0	2.719812e-02	0	15	0	142	2		0	0	0	0	0	2	1	0.998194	11	688	0	141	2		0	0	0	0	142	2	-1.937952	0	1	0	0		1	0	3	3	1.889409	1	0.240000	3.280000	0.314079	0.150000	0.070000	1.000000	0.140000	0.223489	0.150000	0	1.000000e-01	2.200000e-01
NACA2	342538	broad.mit.edu	37	17	59668349	59668349	+	Missense_Mutation	SNP	C	C	A			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr17:59668349C>A	ENST00000521764.1	-	1	214	c.193G>T	c.(193-195)Ggt>Tgt	p.G65C		NM_199290.3	NP_954984.1	Q9H009	NACA2_HUMAN	nascent polypeptide-associated complex alpha subunit 2			12	all_epithelial(1;3.12e-14)				TTTGCTTTACCGACTGGTTCT	0.483000																								0							SO:0001583	missense			ENST00000521764.1	0	1	hg19	CCDS11630.1	.	.	.	.	.	.	.	.	.	.	T	14.35	2.508495	0.44660	.	.	ENSG00000253506	ENST00000521764	T	0.45276	0.9	0.753	-0.473	0.12112	.	0.000000	0.85682	U	0.000000	T	0.16896	0.0406	N	0.08118	0	0.21220	N	0.999753	B	0.24317	0.101	B	0.24269	0.052	T	0.19321	-1.0309	9	.	.	.	.	5.1442	0.14975	0.0:0.4225:0.0:0.5775	.	65	Q9H009	NACA2_HUMAN	C	65	ENSP00000427802:G65C	.	G	-	1	0	NACA2	57023131	1.000000	0.71417	0.972000	0.41901	0.763000	0.43281	2.566000	0.45948	-0.880000	0.03997	-0.684000	0.03749	GGT		TCGA-YB-A89D-01A-12D-A36O-08	NACA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255437.2	0	0	0	13	839	0	219		0	0	0	0	219	2		0	0	0	0	0	2	1	0.999480	16	823	0	214	2		0	0	0	0	219	2	-1.801669	0	1	0	0		1	0	3	3	1.889409	1	0.240000	3.280000	0.314079	0.140000	0.070000	1.000000	0.140000	0.219665	0.140000	0	1.000000e-01	2.100000e-01
SMAD7	4092	broad.mit.edu	37	18	46448072	46448072	+	Silent	SNP	G	G	T			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr18:46448072G>T	ENST00000262158.2	-	4	1237	c.951C>A	c.(949-951)atC>atA	p.I317I	SMAD7_ENST00000591805.1_Silent_p.I102I|SMAD7_ENST00000585986.1_5'UTR|SMAD7_ENST00000589634.1_Silent_p.I316I	NM_001190821.1|NM_005904.3	NP_001177750.1|NP_005895.1	O15105	SMAD7_HUMAN	SMAD family member 7			10	Colorectal(1;0.0518)				TGCCGCAGCCGATTTTGCTCC	0.557000																								0							SO:0001819	synonymous_variant			ENST00000262158.2	1	0	hg19	CCDS11936.1																																																																																				TCGA-YB-A89D-01A-12D-A36O-08	SMAD7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255906.1	1	0	0	11	193	0	48	0	9.291597e-01	0	83	0	48	2		0	0	0	0	0	2	1	0.998245	11	188	0	47	2		0	0	0	0	48	2	-13.918180	1	0	121412	6	36	1	0	2	2	1.733478	1	0.240000	3.280000	0.240000	0.450000	0.240000	0.750000	0.440000	0.477882	0.450000	0	3.400000e-01	6.000000e-01
SMAD4	4089	broad.mit.edu	37	18	48591918	48591918	+	Missense_Mutation	SNP	C	C	T	rs80338963		TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr18:48591918C>T	ENST00000342988.3	+	9	1619	c.1081C>T	c.(1081-1083)Cgc>Tgc	p.R361C	SMAD4_ENST00000588745.1_Missense_Mutation_p.R265C|SMAD4_ENST00000398417.2_Missense_Mutation_p.R361C	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	p.0?(36)|p.R361C(3)|p.R361S(2)|p.?(2)		454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)			TGGAGGAGATCGCTTTTGTTT	0.413000																								43	Whole gene deletion(36)|Substitution - Missense(5)|Unknown(2)	GRCh37	CM040450|CM041789|CM981228	SMAD4	M	rs80338963	SO:0001583	missense			ENST00000342988.3	1	1	hg19	CCDS11950.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.820743	0.90873	.	.	ENSG00000141646	ENST00000342988;ENST00000544926;ENST00000398417	D;D	0.98164	-4.76;-4.76	5.86	5.86	0.93980	SMAD domain-like (1);SMAD/FHA domain (1);SMAD domain, Dwarfin-type (3);	0.000000	0.85682	D	0.000000	D	0.99275	0.9747	M	0.94021	3.485	0.80722	A	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99157	1.0860	9	0.87932	D	0	.	18.9646	0.92691	0.0:1.0:0.0:0.0	.	361	Q13485	SMAD4_HUMAN	C	361	ENSP00000341551:R361C;ENSP00000381452:R361C	ENSP00000341551:R361C	R	+	1	0	SMAD4	46845916	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.718000	0.61930	2.771000	0.95319	0.563000	0.77884	CGC		TCGA-YB-A89D-01A-12D-A36O-08	SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	1	0	1	82	287	0	97	1	9.999875e-01	15	46	0	97	2	1	1	122	376	0	801	2	1	1.000000	78	284	0	96	2		0	0	0	0	97	2	-4.091014	1	1	0	0		1	0	2	2	1.733478	1	0.240000	3.280000	0.240000	0.990000	0.990000	1.000000	1.000000	1.000000	0.990000	1	9.900000e-01	1
ARHGAP35	2909	broad.mit.edu	37	19	47424922	47424922	+	Missense_Mutation	SNP	G	G	T			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr19:47424922G>T	ENST00000404338.3	+	1	2990	c.2990G>T	c.(2989-2991)cGa>cTa	p.R997L		NM_004491.4	NP_004482.4	Q9NRY4	RHG35_HUMAN	Rho GTPase activating protein 35	p.R997Q(1)							AGCCTGTTTCGAGAAGACACA	0.478000																								1	Substitution - Missense(1)						SO:0001583	missense			ENST00000404338.3	0	1	hg19	CCDS46127.1	.	.	.	.	.	.	.	.	.	.	G	15.63	2.889137	0.52014	.	.	ENSG00000160007	ENST00000317082;ENST00000404338	T	0.08370	3.1	5.76	5.76	0.90799	.	0.061993	0.64402	D	0.000005	T	0.11239	0.0274	L	0.43152	1.355	0.43678	D	0.996117	P	0.41624	0.757	P	0.47299	0.543	T	0.17531	-1.0366	10	0.11794	T	0.64	-7.3842	12.1257	0.53915	0.0796:0.0:0.9204:0.0	.	997	Q9NRY4-2	.	L	997	ENSP00000385720:R997L	ENSP00000324820:R997L	R	+	2	0	ARHGAP35	52116762	0.993000	0.37304	0.999000	0.59377	0.995000	0.86356	7.298000	0.78815	2.726000	0.93360	0.655000	0.94253	CGA		TCGA-YB-A89D-01A-12D-A36O-08	ARHGAP35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466652.1	0	0	0	9	410	0	59	0	9.096148e-02	0	21	0	59	2		0	0	0	0	0	2	1	0.993945	9	405	0	59	2		0	0	0	0	59	2	-3.262300	1	1	0	0		1	2	2	4	2.130821	1	0.240000	3.280000	0.384715	0.230000	0.100000	0.440000	0.230000	0.250976	0.230000	0	1.600000e-01	3.200000e-01
ZNF497	162968	broad.mit.edu	37	19	58867557	58867557	+	Missense_Mutation	SNP	C	C	T			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr19:58867557C>T	ENST00000311044.3	-	3	1633	c.1445G>A	c.(1444-1446)cGt>cAt	p.R482H	CTD-2619J13.8_ENST00000599109.1_RNA|A1BG-AS1_ENST00000594950.1_RNA|ZNF497_ENST00000425453.3_Missense_Mutation_p.R482H|A1BG-AS1_ENST00000599728.1_RNA|A1BG-AS1_ENST00000595302.1_RNA|CTD-2619J13.9_ENST00000599952.1_RNA|A1BG-AS1_ENST00000593374.1_RNA|A1BG-AS1_ENST00000600379.1_RNA|A1BG_ENST00000263100.3_5'Flank|A1BG-AS1_ENST00000600686.1_RNA|A1BG-AS1_ENST00000593960.1_RNA	NM_198458.2	NP_940860.2	Q6ZNH5	ZN497_HUMAN	zinc finger protein 497			7		all_cancers(17;3.11e-12)|all_epithelial(17;9.43e-09)|Colorectal(82;0.000256)|Lung NSC(17;0.000607)|all_lung(17;0.0024)|all_neural(62;0.0412)|Ovarian(87;0.156)			GAGGTTGCAACGGTGGCTGAA	0.697000																								0							SO:0001583	missense			ENST00000311044.3	1	1	hg19	CCDS12977.1	.	.	.	.	.	.	.	.	.	.	C	14.00	2.405179	0.42613	.	.	ENSG00000174586	ENST00000311044;ENST00000425453	T;T	0.36157	1.27;1.27	1.01	-0.157	0.13387	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.31136	0.0787	L	0.38531	1.155	0.09310	N	1	D	0.65815	0.995	P	0.52031	0.688	T	0.13361	-1.0512	9	0.36615	T	0.2	.	2.4784	0.04581	0.0:0.4377:0.3307:0.2316	.	482	Q6ZNH5	ZN497_HUMAN	H	482	ENSP00000311183:R482H;ENSP00000402815:R482H	ENSP00000311183:R482H	R	-	2	0	ZNF497	63559369	0.000000	0.05858	0.268000	0.24571	0.241000	0.25554	-1.396000	0.02513	-0.011000	0.14247	0.195000	0.17529	CGT		TCGA-YB-A89D-01A-12D-A36O-08	ZNF497-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466942.2	1	0	1	24	98	0	28	1	1.856671e-01	2	2	0	28	2		0	0	0	0	0	2	1	1.000000	23	95	0	26	2		0	0	0	0	28	2	-3.619874	1	1	120612	1	25	1	2	2	4	2.134925	1	0.240000	3.280000	0.385908	0.990000	0.990000	1.000000	1.000000	0.999979	0.990000	1	9.900000e-01	1
ZNF557	79230	broad.mit.edu	37	19	7082034	7082034	+	Silent	SNP	C	C	A			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr19:7082034C>A	ENST00000439035.2	+	7	616	c.376C>A	c.(376-378)Cga>Aga	p.R126R	ZNF557_ENST00000414706.1_Silent_p.R133R|ZNF557_ENST00000252840.6_Silent_p.R133R			Q8N988	ZN557_HUMAN	zinc finger protein 557			17					GCATGTTTTTCGAAAAGAACA	0.348000																								0							SO:0001819	synonymous_variant			ENST00000439035.2	0	1	hg19	CCDS45945.1																																																																																				TCGA-YB-A89D-01A-12D-A36O-08	ZNF557-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458502.1	0	0	0	10	488	0	78	0	5.002193e-03	0	5	0	78	2		0	0	0	0	0	2	1	0.996607	9	479	0	76	2		0	0	0	0	78	2	-3.037117	1	1	0	0		1	2	2	4	2.120974	1	0.240000	3.280000	0.381107	0.210000	0.100000	1.000000	0.200000	0.253852	0.210000	0	1.500000e-01	3.000000e-01
OR7G3	390883	broad.mit.edu	37	19	9237378	9237378	+	Silent	SNP	C	C	A			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr19:9237378C>A	ENST00000305444.2	-	1	248	c.249G>T	c.(247-249)gtG>gtT	p.V83V		NM_001001958.1	NP_001001958.1	Q8NG95	OR7G3_HUMAN	olfactory receptor, family 7, subfamily G, member 3			15					CCTGGATGTTCACCAGCATCT	0.502000																								0							SO:0001819	synonymous_variant			ENST00000305444.2	0	1	hg19	CCDS32899.1																																																																																				TCGA-YB-A89D-01A-12D-A36O-08	OR7G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384611.1	0	0	0	12	703	0	136		0	0	0	0	136	2		0	0	0	0	0	2	1	0.999057	12	694	0	136	2		0	0	0	0	136	2	-2.671318	1	1	0	0		1	2	2	4	2.120974	1	0.240000	3.280000	0.381107	0.170000	0.080000	1.000000	0.160000	0.216064	0.170000	0	1.200000e-01	2.500000e-01
CSDE1	7812	broad.mit.edu	37	1	115282502	115282502	+	Missense_Mutation	SNP	C	C	A			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr1:115282502C>A	ENST00000358528.4	-	3	436	c.10G>T	c.(10-12)Gat>Tat	p.D4Y	CSDE1_ENST00000438362.2_Missense_Mutation_p.D50Y|CSDE1_ENST00000261443.5_Missense_Mutation_p.D4Y|CSDE1_ENST00000530886.1_Intron|CSDE1_ENST00000339438.6_Missense_Mutation_p.D4Y|CSDE1_ENST00000534699.1_Missense_Mutation_p.D4Y|CSDE1_ENST00000369530.1_Missense_Mutation_p.D50Y	NM_001007553.2	NP_001007554.1	O75534	CSDE1_HUMAN	cold shock domain containing E1, RNA-binding			51	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;2.21e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)			AGGTTTGGATCAAAGCTCATC	0.343000																								0							SO:0001583	missense			ENST00000358528.4	0	1	hg19	CCDS30812.1	.	.	.	.	.	.	.	.	.	.	C	18.77	3.695537	0.68386	.	.	ENSG00000009307	ENST00000339438;ENST00000438362;ENST00000358528;ENST00000261443;ENST00000369530;ENST00000534699;ENST00000534389;ENST00000525878;ENST00000525970	.	.	.	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	T	0.69459	0.3113	L	0.36672	1.1	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.85130	0.997;0.993;0.997	T	0.71167	-0.4672	9	0.87932	D	0	-4.3184	20.4324	0.99085	0.0:1.0:0.0:0.0	.	50;4;50	E9PGZ0;O75534;G5E9Q2	.;CSDE1_HUMAN;.	Y	4;50;4;4;50;4;4;4;4	.	ENSP00000261443:D4Y	D	-	1	0	CSDE1	115084025	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.487000	0.81328	2.833000	0.97629	0.585000	0.79938	GAT		TCGA-YB-A89D-01A-12D-A36O-08	CSDE1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033397.1	0	0	0	16	1384	0	342	0	8.314225e-01	0	283	0	342	2		0	0	0	0	0	2	1	0.999922	16	1366	0	340	2		0	0	0	0	342	2	-2.841673	1	1	0	0		1	1	2	3	1.992567	1	0.240000	3.280000	0.321429	0.100000	0.050000	0.170000	0.120000	0.113012	0.100000	0	7.000000e-02	1.400000e-01
NGF	4803	broad.mit.edu	37	1	115829233	115829233	+	Missense_Mutation	SNP	G	G	A			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr1:115829233G>A	ENST00000369512.2	-	3	352	c.184C>T	c.(184-186)Cgc>Tgc	p.R62C	RP4-663N10.1_ENST00000425449.1_RNA	NM_002506.2	NP_002497.2	P01138	NGF_HUMAN	nerve growth factor (beta polypeptide)			13	Lung SC(450;0.211)	all_cancers(81;1.07e-06)|all_epithelial(167;4.43e-06)|all_lung(203;2.86e-05)|Lung NSC(69;4.99e-05)		Clenbuterol(DB01407)	CCCGCCACGCGTGCAGCTATC	0.632000																								0							SO:0001583	missense			ENST00000369512.2	0	1	hg19	CCDS882.1	.	.	.	.	.	.	.	.	.	.	G	12.46	1.943321	0.34283	.	.	ENSG00000134259	ENST00000369512	T	0.63417	-0.04	5.06	-0.0542	0.13815	.	0.100578	0.42548	D	0.000686	T	0.58206	0.2106	M	0.77486	2.375	0.09310	N	0.999997	D	0.76494	0.999	P	0.51806	0.68	T	0.63184	-0.6694	10	0.87932	D	0	-22.5746	14.8749	0.70488	0.0:0.0:0.6922:0.3078	.	62	P01138	NGF_HUMAN	C	62	ENSP00000358525:R62C	ENSP00000358525:R62C	R	-	1	0	NGF	115630756	0.066000	0.20996	0.543000	0.28128	0.207000	0.24258	1.510000	0.35790	0.104000	0.17725	0.467000	0.42956	CGC		TCGA-YB-A89D-01A-12D-A36O-08	NGF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032832.1	0	0	0	6	221	0	62	0	1.436973e-02	0	6	0	62	2		0	0	0	0	0	2	1	0.963611	5	217	0	62	2		0	0	0	0	62	2	-7.548142	1	1	121410	2	35	1	1	2	3	1.992567	1	0.240000	3.280000	0.321429	0.260000	0.100000	0.500000	0.240000	0.282652	0.260000	0	1.700000e-01	3.800000e-01
SPAG17	200162	broad.mit.edu	37	1	118598506	118598506	+	Missense_Mutation	SNP	G	G	T			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr1:118598506G>T	ENST00000336338.5	-	19	2637	c.2572C>A	c.(2572-2574)Caa>Aaa	p.Q858K		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17			123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)			ATCCAATCTTGAATAGATTTT	0.323000																								0							SO:0001583	missense			ENST00000336338.5	0	1	hg19	CCDS899.1	.	.	.	.	.	.	.	.	.	.	G	11.99	1.803426	0.31869	.	.	ENSG00000155761	ENST00000336338	T	0.29655	1.56	5.35	3.41	0.39046	.	0.697933	0.14968	N	0.287983	T	0.16171	0.0389	L	0.47716	1.5	0.21878	N	0.999499	P	0.40180	0.705	B	0.41510	0.359	T	0.03993	-1.0986	10	0.45353	T	0.12	.	13.3002	0.60321	0.0:0.4907:0.5093:0.0	.	858	Q6Q759	SPG17_HUMAN	K	858	ENSP00000337804:Q858K	ENSP00000337804:Q858K	Q	-	1	0	SPAG17	118400029	1.000000	0.71417	1.000000	0.80357	0.500000	0.33767	1.567000	0.36407	0.770000	0.33336	0.585000	0.79938	CAA		TCGA-YB-A89D-01A-12D-A36O-08	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	0	0	0	12	843	0	170		0	0	0	0	170	2		0	0	0	0	0	2	1	0.999041	13	831	0	168	2		0	0	0	0	170	2	-2.842500	1	1	0	0		1	1	2	3	1.992567	1	0.240000	3.280000	0.321429	0.130000	0.060000	0.220000	0.120000	0.141224	0.130000	0	9.000000e-02	1.800000e-01
SPAG17	200162	broad.mit.edu	37	1	118616493	118616493	+	Missense_Mutation	SNP	G	G	T	rs146282295		TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr1:118616493G>T	ENST00000336338.5	-	17	2434	c.2369C>A	c.(2368-2370)cCg>cAg	p.P790Q		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17			123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)			CAGTACTTTCGGTTTAAAATG	0.428000																								0							SO:0001583	missense			ENST00000336338.5	0	1	hg19	CCDS899.1	.	.	.	.	.	.	.	.	.	.	G	19.44	3.828388	0.71143	.	.	ENSG00000155761	ENST00000336338	T	0.28454	1.61	5.35	5.35	0.76521	.	0.100758	0.64402	D	0.000001	T	0.50871	0.1641	M	0.71581	2.175	0.37958	D	0.932887	D	0.89917	1.0	D	0.91635	0.999	T	0.54275	-0.8318	10	0.72032	D	0.01	.	19.4213	0.94723	0.0:0.0:1.0:0.0	.	790	Q6Q759	SPG17_HUMAN	Q	790	ENSP00000337804:P790Q	ENSP00000337804:P790Q	P	-	2	0	SPAG17	118418016	1.000000	0.71417	0.954000	0.39281	0.901000	0.52897	5.245000	0.65405	2.669000	0.90835	0.650000	0.86243	CCG		TCGA-YB-A89D-01A-12D-A36O-08	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	0	0	0	10	635	0	164		0	0	0	0	164	2		0	0	0	0	0	2	1	0.996711	10	627	0	163	2		0	0	0	0	164	2	-2.060858	0	1	0	0		1	1	2	3	1.992567	1	0.240000	3.280000	0.321429	0.140000	0.070000	0.260000	0.150000	0.158155	0.140000	0	1.000000e-01	2.000000e-01
S100A10	6281	broad.mit.edu	37	1	151958650	151958650	+	Missense_Mutation	SNP	G	G	T			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08			G	T	G	G		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr1:151958650G>T	ENST00000368811.3	-	2	716	c.57C>A	c.(55-57)ttC>ttA	p.F19L	S100A10_ENST00000368809.1_Missense_Mutation_p.F19L|S100A10_ENST00000478574.1_5'UTR	NM_002966.2	NP_002957.1	P60903	S10AA_HUMAN	S100 calcium binding protein A10			6	Melanoma(130;0.0648)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.246)		TATCCCCAGCGAATTTGTGAA	0.403000																								0							SO:0001583	missense			ENST00000368811.3	1	0	hg19	CCDS1008.1	.	.	.	.	.	.	.	.	.	.	G	19.13	3.768048	0.69878	.	.	ENSG00000197747	ENST00000368811;ENST00000368809	T;T	0.09723	2.95;2.95	6.16	4.99	0.66335	S100/CaBP-9k-type, calcium binding, subdomain (1);EF-hand-like domain (1);	0.054288	0.85682	D	0.000000	T	0.08891	0.0220	.	.	.	0.37602	D	0.92058	P	0.42556	0.783	P	0.47786	0.557	T	0.03423	-1.1038	9	0.87932	D	0	.	7.8152	0.29254	0.8401:0.0:0.1599:0.0	.	19	P60903	S10AA_HUMAN	L	19	ENSP00000357801:F19L;ENSP00000357799:F19L	ENSP00000357799:F19L	F	-	3	2	S100A10	150225274	1.000000	0.71417	1.000000	0.80357	0.812000	0.45895	1.787000	0.38704	1.142000	0.42291	-0.300000	0.09419	TTC		TCGA-YB-A89D-01A-12D-A36O-08	S100A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036673.1	1	0	0	37	892	0	178	0	1	1	3634	0	178	2		0	0	0	0	0	2	1	1.000000	37	883	0	173	2		0	0	0	0	178	2	-3.486754	1	1	0	0		1	1	2	3	1.984441	1	0.240000	3.280000	0.321429	0.370000	0.260000	0.500000	0.360000	0.380085	0.370000	0	3.100000e-01	4.400000e-01
EDEM3	80267	broad.mit.edu	37	1	184675862	184675862	+	Silent	SNP	G	G	T			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr1:184675862G>T	ENST00000318130.8	-	18	2384	c.2118C>A	c.(2116-2118)atC>atA	p.I706I	EDEM3_ENST00000367512.3_Silent_p.I663I|EDEM3_ENST00000466392.1_5'UTR	NM_025191.3	NP_079467.3	Q9BZQ6	EDEM3_HUMAN	ER degradation enhancer, mannosidase alpha-like 3	p.I663I(1)		30					GTATCAGTGCGATTTTTCCCA	0.433000																								1	Substitution - coding silent(1)						SO:0001819	synonymous_variant			ENST00000318130.8	1	0	hg19	CCDS1363.2																																																																																				TCGA-YB-A89D-01A-12D-A36O-08	EDEM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085785.3	1	0	0	15	307	0	56	0	6.906616e-01	0	50	0	56	2		0	0	0	0	0	2	1	0.999872	14	305	0	55	2		0	0	0	0	56	2	-16.143300	1	0	0	0		1	1	2	3	1.992118	1	0.240000	3.280000	0.321429	0.440000	0.250000	0.680000	0.430000	0.457889	0.440000	0	3.400000e-01	5.600000e-01
HMCN1	83872	broad.mit.edu	37	1	185833685	185833685	+	Silent	SNP	T	T	G			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr1:185833685T>G	ENST00000271588.4	+	3	652	c.423T>G	c.(421-423)gtT>gtG	p.V141V	HMCN1_ENST00000367492.2_Silent_p.V141V	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1			308					TCATCTATGTTTTCACTGATG	0.438000																								0							SO:0001819	synonymous_variant			ENST00000271588.4	0	1	hg19	CCDS30956.1																																																																																				TCGA-YB-A89D-01A-12D-A36O-08	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	0	0	0	5	315	0	64	0	2.343998e-03	0	4	0	64	2		0	0	0	0	0	2	1	0.936463	5	312	0	64	2		0	0	0	0	64	2	-5.863957	1	1	0	0		1	1	2	3	1.992118	1	0.240000	3.280000	0.321429	0.150000	0.050000	0.320000	0.150000	0.172765	0.150000	0	9.000000e-02	2.400000e-01
HMCN1	83872	broad.mit.edu	37	1	185931765	185931765	+	Silent	SNP	C	C	T			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr1:185931765C>T	ENST00000271588.4	+	12	2173	c.1944C>T	c.(1942-1944)aaC>aaT	p.N648N	HMCN1_ENST00000367492.2_Silent_p.N648N|HMCN1_ENST00000485744.1_3'UTR	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1			308					GGACCGTTAACGATATGTTTA	0.413000																								0							SO:0001819	synonymous_variant			ENST00000271588.4	0	1	hg19	CCDS30956.1																																																																																				TCGA-YB-A89D-01A-12D-A36O-08	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	0	0	0	15	1014	0	201	0	2.449838e-03	0	5	0	201	2		0	0	0	0	0	2	1	0.999857	17	1001	0	199	2		0	0	0	0	201	2	-2.642559	1	1	121412	5	41	1	1	2	3	1.992118	1	0.240000	3.280000	0.321429	0.130000	0.070000	0.220000	0.140000	0.144540	0.130000	0	1.000000e-01	1.800000e-01
KCNK2	3776	broad.mit.edu	37	1	215408472	215408472	+	Missense_Mutation	SNP	T	T	C			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr1:215408472T>C	ENST00000444842.2	+	7	1415	c.1265T>C	c.(1264-1266)aTt>aCt	p.I422T	KCNK2_ENST00000391894.2_Missense_Mutation_p.I407T|KCNK2_ENST00000391895.2_Missense_Mutation_p.I418T	NM_001017425.2|NM_014217.3	NP_001017425.2|NP_055032.1	O95069	KCNK2_HUMAN	potassium channel, subfamily K, member 2			30				Dofetilide(DB00204)|Dronedarone(DB04855)	ATTGCTGTGATTGAGAACATC	0.438000																								0							SO:0001583	missense			ENST00000444842.2	0	1	hg19	CCDS41467.1	.	.	.	.	.	.	.	.	.	.	T	16.60	3.167433	0.57476	.	.	ENSG00000082482	ENST00000391895;ENST00000391894;ENST00000444842	T;T;T	0.26518	1.73;1.76;1.73	5.63	5.63	0.86233	.	0.385177	0.29565	N	0.011799	T	0.21347	0.0514	L	0.27053	0.805	0.58432	D	0.999999	P;P;P	0.40731	0.728;0.608;0.728	B;B;B	0.37888	0.26;0.133;0.26	T	0.03157	-1.1066	10	0.87932	D	0	.	15.8309	0.78749	0.0:0.0:0.0:1.0	.	407;422;418	O95069-2;O95069;O95069-3	.;KCNK2_HUMAN;.	T	418;407;422	ENSP00000375765:I418T;ENSP00000375764:I407T;ENSP00000394033:I422T	ENSP00000375764:I407T	I	+	2	0	KCNK2	213475095	1.000000	0.71417	0.996000	0.52242	0.991000	0.79684	7.502000	0.81614	2.149000	0.67028	0.402000	0.26972	ATT		TCGA-YB-A89D-01A-12D-A36O-08	KCNK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089856.2	0	0	0	7	547	0	104	0	2.234889e-03	0	5	0	104	2		0	0	0	0	0	2	1	0.980084	7	542	0	103	2		0	0	0	0	104	2	-6.290299	1	1	0	0		1	1	2	3	1.982112	0	0.240000	3.280000	0.321429	0.120000	0.040000	0.230000	0.120000	0.133781	0.120000	0	8.000000e-02	1.800000e-01
EPB41	2035	broad.mit.edu	37	1	29359683	29359683	+	Missense_Mutation	SNP	C	C	A			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr1:29359683C>A	ENST00000343067.4	+	9	1418	c.1291C>A	c.(1291-1293)Cgc>Agc	p.R431S	EPB41_ENST00000398863.2_Missense_Mutation_p.R431S|EPB41_ENST00000373797.1_Missense_Mutation_p.R431S|EPB41_ENST00000349460.4_Missense_Mutation_p.R222S|EPB41_ENST00000356093.2_Missense_Mutation_p.R431S|EPB41_ENST00000347529.3_Missense_Mutation_p.R396S|EPB41_ENST00000373798.1_Missense_Mutation_p.R431S|EPB41_ENST00000373800.3_Missense_Mutation_p.R222S	NM_001166005.1	NP_001159477.1	P11171	41_HUMAN	erythrocyte membrane protein band 4.1			14		Colorectal(325;3.46e-05)|Prostate(1639;0.000244)|Lung NSC(340;0.00328)|all_lung(284;0.00412)|Breast(348;0.00765)|all_neural(195;0.0199)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)|Medulloblastoma(700;0.123)			GAGAATTAACCGCTTCCCTTG	0.408000																								0							SO:0001583	missense			ENST00000343067.4	0	1	hg19	CCDS53288.1	.	.	.	.	.	.	.	.	.	.	C	29.3	4.991544	0.93106	.	.	ENSG00000159023	ENST00000358989;ENST00000343067;ENST00000356093;ENST00000398863;ENST00000398861;ENST00000398865;ENST00000349460;ENST00000373800;ENST00000347529;ENST00000373798;ENST00000373797	D;D;D;D;D;D;D;D	0.85773	-2.03;-2.03;-2.03;-2.03;-2.03;-2.03;-2.03;-2.03	5.97	5.97	0.96955	FERM, C-terminal PH-like domain (1);FERM domain (1);Pleckstrin homology-type (1);	0.000000	0.85682	D	0.000000	D	0.88998	0.6590	L	0.39566	1.225	0.80722	D	1	D;P;D;D;D;D;D;D;D;D	0.89917	1.0;0.859;0.997;0.999;0.991;0.996;1.0;0.986;0.998;1.0	D;P;D;D;P;P;D;P;D;D	0.91635	0.99;0.765;0.932;0.984;0.83;0.888;0.999;0.895;0.984;0.999	D	0.89328	0.3645	10	0.87932	D	0	.	14.2724	0.66159	0.1486:0.8514:0.0:0.0	.	325;431;431;431;431;431;448;396;222;222	E9PEX0;E9PEW9;C9JTS2;P11171;P11171-2;P11171-7;Q59F12;P11171-5;P11171-4;P11171-3	.;.;.;41_HUMAN;.;.;.;.;.;.	S	448;431;431;431;325;431;222;222;396;431;431	ENSP00000345259:R431S;ENSP00000348397:R431S;ENSP00000381839:R431S;ENSP00000317597:R222S;ENSP00000362906:R222S;ENSP00000290100:R396S;ENSP00000362904:R431S;ENSP00000362903:R431S	ENSP00000345259:R431S	R	+	1	0	EPB41	29232270	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.696000	0.61774	2.834000	0.97654	0.650000	0.86243	CGC		TCGA-YB-A89D-01A-12D-A36O-08	EPB41-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010312.1	0	0	0	7	463	0	96	0	1.851319e-02	0	12	0	96	2		0	0	0	0	0	2	1	0.980167	7	459	0	96	2		0	0	0	0	96	2	-2.874733	1	1	0	0		1	1	2	3	1.992567	1	0.240000	3.280000	0.321429	0.140000	0.050000	0.270000	0.150000	0.157478	0.140000	0	9.000000e-02	2.100000e-01
WDR78	79819	broad.mit.edu	37	1	67337143	67337143	+	Missense_Mutation	SNP	C	C	A			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr1:67337143C>A	ENST00000371026.3	-	6	905	c.850G>T	c.(850-852)Gac>Tac	p.D284Y	WDR78_ENST00000431318.1_Missense_Mutation_p.D30Y|WDR78_ENST00000371022.3_Missense_Mutation_p.D284Y|WDR78_ENST00000371023.3_Missense_Mutation_p.D284Y	NM_024763.4	NP_079039.4	Q5VTH9	WDR78_HUMAN	WD repeat domain 78			32					ACATATAGGTCATTGCCTAAT	0.318000																								0							SO:0001583	missense			ENST00000371026.3	1	1	hg19	CCDS635.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.34|14.34	2.507082|2.507082	0.44558|0.44558	.|.	.|.	ENSG00000152763|ENSG00000152763	ENST00000371026;ENST00000431318;ENST00000464352;ENST00000371023;ENST00000371022|ENST00000469450	T;T;T;T;T|.	0.79554|.	-0.23;-1.28;-0.66;1.57;0.19|.	5.86|5.86	5.86|5.86	0.93980|0.93980	.|.	0.047040|.	0.85682|.	D|.	0.000000|.	T|.	0.79417|.	0.4442|.	M|M	0.82323|0.82323	2.585|2.585	0.58432|0.58432	D|D	0.999996|0.999996	D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0|.	D;D;D;D|.	0.91635|.	0.998;0.999;0.994;0.994|.	T|.	0.79349|.	-0.1840|.	10|.	0.87932|.	D|.	0|.	-28.0743|-28.0743	18.9441|18.9441	0.92615|0.92615	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	30;284;284;284|.	Q5VTH9-3;Q5TAD8;A0AVI9;Q5VTH9|.	.;.;.;WDR78_HUMAN|.	Y|L	284;30;50;284;284|17	ENSP00000360065:D284Y;ENSP00000393182:D30Y;ENSP00000433682:D50Y;ENSP00000360062:D284Y;ENSP00000360061:D284Y|.	ENSP00000360061:D284Y|.	D|X	-|-	1|2	0|2	WDR78|WDR78	67109731|67109731	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.063000|0.063000	0.16089|0.16089	4.342000|4.342000	0.59341|0.59341	2.763000|2.763000	0.94921|0.94921	0.650000|0.650000	0.86243|0.86243	GAC|TGA		TCGA-YB-A89D-01A-12D-A36O-08	WDR78-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025404.1	1	0	0	83	819	0	146	0	8.708060e-03	0	2	0	146	2		0	0	0	0	0	2	1	1.000000	83	811	0	145	2		0	0	0	0	146	2	-19.987740	1	1	0	0		1	1	2	3	1.992567	1	0.240000	3.280000	0.321429	0.850000	0.690000	1.000000	1.000000	0.861967	0.850000	1	7.600000e-01	9.500000e-01
CST11	140880	broad.mit.edu	37	20	23433311	23433311	+	Missense_Mutation	SNP	G	G	C			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr20:23433311G>C	ENST00000377009.3	-	1	171	c.138C>G	c.(136-138)gaC>gaG	p.D46E	CST11_ENST00000377007.3_Missense_Mutation_p.D46E	NM_130794.1	NP_570612.1	Q9H112	CST11_HUMAN	cystatin 11			14	Colorectal(13;0.0431)|Lung NSC(19;0.235)				ACTGCAAGCTGTCCTTCGCAT	0.473000																								0							SO:0001583	missense			ENST00000377009.3	0	1	hg19	CCDS13155.1	.	.	.	.	.	.	.	.	.	.	G	0.034	-1.315401	0.01331	.	.	ENSG00000125831	ENST00000377009;ENST00000377007	T;T	0.20881	2.04;2.04	3.86	-7.72	0.01250	Proteinase inhibitor I25, cystatin (2);	1.801240	0.02192	N	0.061416	T	0.07188	0.0182	N	0.12182	0.205	0.09310	N	1	B;B	0.14805	0.009;0.011	B;B	0.18871	0.023;0.022	T	0.32903	-0.9889	10	0.02654	T	1	-0.6315	0.5297	0.00626	0.3409:0.2761:0.1774:0.2056	.	46;46	Q9H112-2;Q9H112	.;CST11_HUMAN	E	46	ENSP00000366208:D46E;ENSP00000366206:D46E	ENSP00000366206:D46E	D	-	3	2	CST11	23381311	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.747000	0.04823	-1.825000	0.01207	-0.142000	0.14014	GAC		TCGA-YB-A89D-01A-12D-A36O-08	CST11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078314.1	0	0	0	10	735	0	155		0	0	0	0	155	2		0	0	0	0	0	2	1	0.996794	10	730	0	152	2		0	0	0	0	155	2	-2.717826	1	1	121412	1	34	1	2	2	4	2.163192	1	0.240000	3.280000	0.387097	0.140000	0.060000	0.250000	0.130000	0.151828	0.140000	0	9.000000e-02	2.000000e-01
CTCFL	140690	broad.mit.edu	37	20	56094287	56094287	+	Missense_Mutation	SNP	G	G	A			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr20:56094287G>A	ENST00000608263.1	-	3	1562	c.901C>T	c.(901-903)Cgg>Tgg	p.R301W	CTCFL_ENST00000433949.3_Missense_Mutation_p.R96W|CTCFL_ENST00000371196.2_Missense_Mutation_p.R301W|CTCFL_ENST00000502686.2_Missense_Mutation_p.R39W|CTCFL_ENST00000243914.3_Missense_Mutation_p.R301W|CTCFL_ENST00000609232.1_Missense_Mutation_p.R301W|CTCFL_ENST00000423479.3_Missense_Mutation_p.R301W|CTCFL_ENST00000608425.1_Missense_Mutation_p.R301W|CTCFL_ENST00000608858.1_5'UTR|CTCFL_ENST00000432255.2_Missense_Mutation_p.R301W|CTCFL_ENST00000608903.1_Missense_Mutation_p.R39W|CTCFL_ENST00000481655.2_Missense_Mutation_p.R301W|CTCFL_ENST00000539382.1_Missense_Mutation_p.R96W|CTCFL_ENST00000608158.1_Missense_Mutation_p.R301W|CTCFL_ENST00000429804.3_Missense_Mutation_p.R301W|CTCFL_ENST00000608440.1_Missense_Mutation_p.R301W|CTCFL_ENST00000422869.2_Missense_Mutation_p.R301W	NM_001269041.1	NP_001255970.1	Q8NI51	CTCFL_HUMAN	CCCTC-binding factor (zinc finger protein)-like			58	Lung NSC(12;0.00132)|all_lung(29;0.00433)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;3.95e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.09e-07)		ACATGGTTCCGCAGCAGAGTG	0.453000																								0							SO:0001583	missense			ENST00000608263.1	0	1	hg19	CCDS13459.1	.	.	.	.	.	.	.	.	.	.	G	13.44	2.238725	0.39598	.	.	ENSG00000124092	ENST00000423479;ENST00000243914;ENST00000371196;ENST00000429804;ENST00000433949;ENST00000502686;ENST00000422109;ENST00000426658;ENST00000432255;ENST00000539382;ENST00000422869	T;T;T;T;T;T;T;T;T;T;T	0.08282	3.11;3.11;3.11;3.11;3.11;3.11;3.11;3.11;3.11;3.11;3.11	5.25	0.582	0.17412	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.40554	N	0.001079	T	0.25531	0.0621	M	0.69523	2.12	0.38434	D	0.946527	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	0.97110	1.0;1.0;0.995;1.0;1.0;1.0;1.0;1.0	T	0.10847	-1.0612	10	0.72032	D	0.01	-42.7671	14.3281	0.66534	0.0:0.0:0.3805:0.6195	.	301;301;301;301;301;301;301;301	A6XGM3;A6XGM0;A6XGM9;A6XGM8;A6XGM2;E7EUE3;A6XGL8;Q8NI51	.;.;.;.;.;.;.;CTCFL_HUMAN	W	301;301;301;301;301;39;301;301;301;96;301	ENSP00000415579:R301W;ENSP00000243914:R301W;ENSP00000360239:R301W;ENSP00000415329:R301W;ENSP00000392034:R301W;ENSP00000437999:R39W;ENSP00000413713:R301W;ENSP00000403369:R301W;ENSP00000409344:R301W;ENSP00000439998:R96W;ENSP00000399061:R301W	ENSP00000243914:R301W	R	-	1	2	CTCFL	55527693	0.611000	0.26992	0.073000	0.20177	0.072000	0.16883	0.855000	0.27805	0.255000	0.21593	-0.293000	0.09583	CGG		TCGA-YB-A89D-01A-12D-A36O-08	CTCFL-019	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000472040.1	0	0	0	6	495	0	87		0	0	0	0	87	2		0	0	0	0	0	2	1	0.964070	6	490	0	87	2		0	0	0	0	87	2	-2.774029	1	1	121412	2	33	1	2	2	4	2.163192	1	0.240000	3.280000	0.387097	0.130000	0.040000	0.260000	0.120000	0.143390	0.130000	0	8.000000e-02	2.000000e-01
ZBP1	81030	broad.mit.edu	37	20	56189968	56189968	+	Silent	SNP	G	G	T			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr20:56189968G>T	ENST00000371173.3	-	4	654	c.477C>A	c.(475-477)tcC>tcA	p.S159S	ZBP1_ENST00000538947.1_5'Flank|ZBP1_ENST00000340462.4_Silent_p.S136S|ZBP1_ENST00000343535.4_Silent_p.S159S|ZBP1_ENST00000541799.1_Silent_p.S159S|ZBP1_ENST00000395822.3_Silent_p.S84S	NM_001160417.1|NM_030776.2	NP_001153889.1|NP_110403.2	Q9H171	ZBP1_HUMAN	Z-DNA binding protein 1			27	Lung NSC(12;0.000545)|all_lung(29;0.00195)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;7.87e-13)|Epithelial(14;3.26e-09)|all cancers(14;3.62e-08)		TCCATGCTTTGGACTGCTCAT	0.557000																								0							SO:0001819	synonymous_variant			ENST00000371173.3	0	1	hg19	CCDS13461.1																																																																																				TCGA-YB-A89D-01A-12D-A36O-08	ZBP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079849.1	0	0	0	10	732	0	147	0	6.219297e-03	0	8	0	147	2		0	0	0	0	0	2	1	0.996726	9	725	0	144	2		0	0	0	0	147	2	-2.240626	0	1	0	0		1	2	2	4	2.163192	1	0.240000	3.280000	0.387097	0.140000	0.060000	0.250000	0.130000	0.152439	0.140000	0	1.000000e-01	2.000000e-01
MYO18B	84700	broad.mit.edu	37	22	26219559	26219559	+	Missense_Mutation	SNP	C	C	T			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr22:26219559C>T	ENST00000407587.2	+	13	2778	c.2609C>T	c.(2608-2610)aCc>aTc	p.T870I	MYO18B_ENST00000335473.7_Missense_Mutation_p.T870I|MYO18B_ENST00000536101.1_Missense_Mutation_p.T870I			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	p.T870I(1)		146					AACACGGCCACCTTCAAGCAC	0.577000																								1	Substitution - Missense(1)						SO:0001583	missense			ENST00000407587.2	1	1	hg19		.	.	.	.	.	.	.	.	.	.	C	13.11	2.139738	0.37728	.	.	ENSG00000133454	ENST00000536101;ENST00000335473;ENST00000407587	T;T;T	0.69040	-0.37;-0.37;-0.37	4.73	3.47	0.39725	Myosin head, motor domain (2);	0.306844	0.29932	N	0.010821	T	0.54806	0.1881	L	0.28776	0.89	0.34621	D	0.718623	P;D;P;D	0.54207	0.708;0.965;0.946;0.957	B;P;P;P	0.52217	0.249;0.693;0.462;0.567	T	0.58864	-0.7561	10	0.13108	T	0.6	.	4.1753	0.10349	0.0:0.6771:0.0:0.3229	.	383;870;870;870	Q8IUG5-2;Q8IUG5;F5GXR6;F5GYU7	.;MY18B_HUMAN;.;.	I	870	ENSP00000441229:T870I;ENSP00000334563:T870I;ENSP00000386096:T870I	ENSP00000334563:T870I	T	+	2	0	MYO18B	24549559	1.000000	0.71417	1.000000	0.80357	0.670000	0.39368	4.574000	0.60900	2.327000	0.79052	0.448000	0.29417	ACC		TCGA-YB-A89D-01A-12D-A36O-08	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	1	0	1	194	540	0	204		0	0	0	0	204	2		0	0	0	0	0	2	1	1.000000	192	530	0	198	2		0	0	0	0	204	2	-20.000000	1	1	0	0		1	0	2	2	1.752359	1	0.240000	3.280000	0.240000	0.990000	0.990000	1.000000	1.000000	1.000000	0.990000	1	9.900000e-01	1
MGAT3	4248	broad.mit.edu	37	22	39884255	39884255	+	Silent	SNP	C	C	A			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr22:39884255C>A	ENST00000341184.6	+	2	1118	c.903C>A	c.(901-903)gtC>gtA	p.V301V		NM_001098270.1|NM_002409.4	NP_001091740.1|NP_002400.3	Q09327	MGAT3_HUMAN	mannosyl (beta-1,4-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase			24	Melanoma(58;0.04)				AGGACGGCGTCTCGCGGCTGC	0.657000																								0							SO:0001819	synonymous_variant			ENST00000341184.6	1	1	hg19	CCDS13994.2																																																																																				TCGA-YB-A89D-01A-12D-A36O-08	MGAT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075039.2	1	0	1	78	527	0	163	1	9.732522e-01	24	16	0	163	2		0	0	0	0	0	2	1	1.000000	77	519	0	162	2		0	0	0	0	163	2	-20.000000	1	1	0	0		1	0	2	2	1.799677	1	0.240000	3.280000	0.240000	0.990000	0.860000	1.000000	1.000000	0.984482	0.990000	1	9.600000e-01	1
MGAT3	4248	broad.mit.edu	37	22	39884489	39884489	+	Silent	SNP	C	C	T			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr22:39884489C>T	ENST00000341184.6	+	2	1352	c.1137C>T	c.(1135-1137)atC>atT	p.I379I		NM_001098270.1|NM_002409.4	NP_001091740.1|NP_002400.3	Q09327	MGAT3_HUMAN	mannosyl (beta-1,4-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase			24	Melanoma(58;0.04)				TGGACGGCATCCGCCTGCGCC	0.647000																								0							SO:0001819	synonymous_variant			ENST00000341184.6	1	1	hg19	CCDS13994.2																																																																																				TCGA-YB-A89D-01A-12D-A36O-08	MGAT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075039.2	1	0	1	47	357	0	105	1	9.847040e-01	36	16	0	105	2		0	0	0	0	0	2	1	1.000000	45	347	0	103	2		0	0	0	0	105	2	-20.000000	1	1	0	0		1	0	2	2	1.799677	1	0.240000	3.280000	0.240000	0.960000	0.720000	1.000000	1.000000	0.934896	0.960000	1	8.400000e-01	1
MGAT3	4248	broad.mit.edu	37	22	39884636	39884636	+	Silent	SNP	C	C	T			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr22:39884636C>T	ENST00000341184.6	+	2	1499	c.1284C>T	c.(1282-1284)atC>atT	p.I428I		NM_001098270.1|NM_002409.4	NP_001091740.1|NP_002400.3	Q09327	MGAT3_HUMAN	mannosyl (beta-1,4-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase			24	Melanoma(58;0.04)				CCGAGGGCATCTACTTCAAGC	0.652000																								0							SO:0001819	synonymous_variant			ENST00000341184.6	1	1	hg19	CCDS13994.2																																																																																				TCGA-YB-A89D-01A-12D-A36O-08	MGAT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075039.2	1	0	1	18	151	0	43	1	9.506031e-01	35	10	0	43	2		0	0	0	0	0	2	1	0.999985	18	149	0	42	2		0	0	0	0	43	2	-20.000000	1	1	0	0		1	0	2	2	1.799677	1	0.240000	3.280000	0.240000	0.880000	0.550000	1.000000	1.000000	0.866172	0.880000	1	7.000000e-01	1
TNRC6B	23112	broad.mit.edu	37	22	40662002	40662002	+	Missense_Mutation	SNP	C	C	T			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr22:40662002C>T	ENST00000454349.2	+	5	1979	c.1768C>T	c.(1768-1770)Cgt>Tgt	p.R590C	TNRC6B_ENST00000402203.1_Intron|TNRC6B_ENST00000335727.9_Missense_Mutation_p.R590C|TNRC6B_ENST00000301923.9_Intron	NM_001162501.1	NP_001155973.1	Q9UPQ9	TNR6B_HUMAN	trinucleotide repeat containing 6B			1					TAACTCTGGCCGTCGGTCGTA	0.527000																								0							SO:0001583	missense			ENST00000454349.2	1	1	hg19	CCDS54533.1	.	.	.	.	.	.	.	.	.	.	C	14.45	2.539333	0.45176	.	.	ENSG00000100354	ENST00000454349;ENST00000400140;ENST00000335727	T;T	0.14022	2.56;2.54	5.53	5.53	0.82687	.	0.106556	0.64402	D	0.000003	T	0.23965	0.0580	N	0.22421	0.69	0.50467	D	0.999871	D;D;D	0.89917	1.0;0.998;0.996	D;B;P	0.76575	0.988;0.446;0.649	T	0.01276	-1.1398	10	0.56958	D	0.05	-4.2093	14.3069	0.66391	0.1485:0.8515:0.0:0.0	.	590;590;590	Q9UPQ9;A8MYY3;Q9UPQ9-1	TNR6B_HUMAN;.;.	C	590	ENSP00000401946:R590C;ENSP00000338371:R590C	ENSP00000338371:R590C	R	+	1	0	TNRC6B	38991948	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.492000	0.53259	2.607000	0.88179	0.555000	0.69702	CGT		TCGA-YB-A89D-01A-12D-A36O-08	TNRC6B-202	KNOWN	basic|CCDS	protein_coding	protein_coding		1	0	1	74	613	0	160	0	9.487944e-02	1	4	0	160	2		0	0	0	0	0	2	1	1.000000	74	600	1	160	15		0	0	0	0	160	2	-3.142702	1	1	0	0		1	0	2	2	1.799677	1	0.240000	3.280000	0.240000	0.890000	0.710000	1.000000	1.000000	0.893756	0.890000	1	7.900000e-01	1
EFCAB6	64800	broad.mit.edu	37	22	44127685	44127685	+	Silent	SNP	C	C	A			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr22:44127685C>A	ENST00000262726.7	-	8	904	c.651G>T	c.(649-651)tcG>tcT	p.S217S	EFCAB6_ENST00000358439.4_Silent_p.S111S|EFCAB6_ENST00000396231.2_Silent_p.S65S|EFCAB6_ENST00000356087.4_Silent_p.S111S	NM_022785.3	NP_073622.2	Q5THR3	EFCB6_HUMAN	EF-hand calcium binding domain 6			68		Ovarian(80;0.0247)|all_neural(38;0.025)			TGTAGTGTTTCGAAAACCTAA	0.333000																								0							SO:0001819	synonymous_variant			ENST00000262726.7	0	1	hg19	CCDS14049.1																																																																																				TCGA-YB-A89D-01A-12D-A36O-08	EFCAB6-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353176.1	0	0	0	13	579	0	105	0	0	0	1	0	105	2		0	0	0	0	0	2	1	0.999538	14	578	0	104	2		0	0	0	0	105	2	-3.292305	1	1	0	0		1	0	2	2	1.770719	1	0.240000	3.280000	0.240000	0.180000	0.100000	0.300000	0.180000	0.195344	0.180000	0	1.300000e-01	2.400000e-01
CPT1B	1375	broad.mit.edu	37	22	51012928	51012928	+	Silent	SNP	G	G	T			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr22:51012928G>T	ENST00000360719.2	-	8	1016	c.879C>A	c.(877-879)atC>atA	p.I293I	CPT1B_ENST00000395650.2_Silent_p.I293I|CPT1B_ENST00000312108.7_Silent_p.I293I|CPT1B_ENST00000440709.1_Silent_p.I293I|CHKB-CPT1B_ENST00000453634.1_3'UTR|CPT1B_ENST00000434492.2_Silent_p.I90I|CPT1B_ENST00000457250.1_Silent_p.I259I|CPT1B_ENST00000405237.3_Silent_p.I293I	NM_001145135.1|NM_152245.2	NP_001138607.1|NP_689451.1	Q92523	CPT1B_HUMAN	carnitine palmitoyltransferase 1B (muscle)			22		all_cancers(38;8.8e-15)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)			TCACAGGCTTGATTTCTTCAC	0.557000													Esophageal Squamous(170;988 1933 25577 30295 48163)											0							SO:0001819	synonymous_variant			ENST00000360719.2	0	1	hg19	CCDS14098.1																																																																																				TCGA-YB-A89D-01A-12D-A36O-08	CPT1B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317264.5	0	0	0	15	559	0	172	0	1.940588e-01	0	29	0	172	2		0	0	0	0	0	2	1	0.999849	14	547	0	169	2		0	0	0	0	172	2	-2.214577	0	1	0	0		1	0	2	2	1.770719	1	0.240000	3.280000	0.240000	0.220000	0.120000	0.340000	0.220000	0.230191	0.220000	0	1.600000e-01	2.800000e-01
CNTNAP5	129684	broad.mit.edu	37	2	125284870	125284870	+	Missense_Mutation	SNP	G	G	T			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr2:125284870G>T	ENST00000431078.1	+	10	1847	c.1483G>T	c.(1483-1485)Gac>Tac	p.D495Y		NM_130773.2	NP_570129.1	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5			176					AGGGTGCCCCGACAATCTCAC	0.443000																								0							SO:0001583	missense			ENST00000431078.1	1	0	hg19	CCDS46401.1	.	.	.	.	.	.	.	.	.	.	G	18.77	3.694209	0.68386	.	.	ENSG00000155052	ENST00000431078	T	0.80033	-1.33	5.67	5.67	0.87782	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.000000	0.48286	D	0.000195	D	0.89536	0.6743	M	0.77820	2.39	0.46416	D	0.999037	D	0.64830	0.994	D	0.64687	0.928	D	0.90164	0.4230	10	0.72032	D	0.01	.	18.7756	0.91910	0.0:0.0:1.0:0.0	.	495	Q8WYK1	CNTP5_HUMAN	Y	495	ENSP00000399013:D495Y	ENSP00000399013:D495Y	D	+	1	0	CNTNAP5	125001340	1.000000	0.71417	0.978000	0.43139	0.994000	0.84299	3.319000	0.51983	2.685000	0.91497	0.650000	0.86243	GAC		TCGA-YB-A89D-01A-12D-A36O-08	CNTNAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330864.3	1	0	0	13	295	0	57		0	0	0	0	57	2		0	0	0	0	0	2	1	0.999501	13	289	0	57	2		0	0	0	0	57	2	-4.145986	1	1	0	0		1	2	2	4	2.162740	1	0.240000	3.280000	0.387097	0.440000	0.240000	0.710000	0.440000	0.464273	0.440000	0	3.300000e-01	5.800000e-01
LRP1B	53353	broad.mit.edu	37	2	141747122	141747122	+	Nonsense_Mutation	SNP	C	C	A			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr2:141747122C>A	ENST00000389484.3	-	17	3720	c.2749G>T	c.(2749-2751)Gaa>Taa	p.E917*	Y_RNA_ENST00000365022.1_RNA	NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B			606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)			TGATTGGATTCATCTTCATTG	0.388000										TSP Lung(27;0.18)			Colon(99;50 2074 2507 20106)											0							SO:0001587	stop_gained			ENST00000389484.3	0	1	hg19	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	C	50	16.335596	0.99861	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	.	.	.	5.69	5.69	0.88448	.	0.000000	0.85682	U	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	20.181	0.98201	0.0:1.0:0.0:0.0	.	.	.	.	X	917;855	.	ENSP00000374135:E917X	E	-	1	0	LRP1B	141463592	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.727000	0.84838	2.840000	0.97914	0.655000	0.94253	GAA		TCGA-YB-A89D-01A-12D-A36O-08	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	0	0	0	15	744	0	153		0	0	0	0	153	2		0	0	0	0	0	2	1	0.999860	15	736	0	152	2		0	0	0	0	153	2	-2.740707	1	1	0	0		1	2	2	4	2.162740	1	0.240000	3.280000	0.387097	0.200000	0.110000	0.330000	0.200000	0.216810	0.200000	0	1.500000e-01	2.700000e-01
TTN	7273	broad.mit.edu	37	2	179445134	179445134	+	Silent	SNP	C	C	A			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr2:179445134C>A	ENST00000591111.1	-	267	62273	c.62049G>T	c.(62047-62049)gtG>gtT	p.V20683V	RP11-171I2.2_ENST00000603521.1_RNA|RP11-171I2.5_ENST00000604215.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN_ENST00000342992.6_Silent_p.V19756V|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000460472.2_Silent_p.V13259V|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000589042.1_Silent_p.V22324V|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000342175.6_Silent_p.V13451V|TTN_ENST00000359218.5_Silent_p.V13384V|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000592600.1_RNA			Q8WZ42	TITIN_HUMAN	titin			1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)		CATATTTGTTCACATTTTCAC	0.363000																								0							SO:0001819	synonymous_variant			ENST00000591111.1	0	1	hg19																																																																																					TCGA-YB-A89D-01A-12D-A36O-08	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	0	0	0	18	783	0	143	0	5.885888e-04	0	2	0	143	2		0	0	0	0	0	2	1	0.999979	16	774	0	141	2		0	0	0	0	143	2	-2.532828	1	1	0	0		1	2	2	4	2.076171	0	0.240000	3.280000	0.367510	0.230000	0.130000	1.000000	0.220000	0.332437	0.230000	0	1.800000e-01	3.400000e-01
TTN	7273	broad.mit.edu	37	2	179458949	179458949	+	Missense_Mutation	SNP	C	C	A			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr2:179458949C>A	ENST00000591111.1	-	247	53472	c.53248G>T	c.(53248-53250)Gac>Tac	p.D17750Y	TTN-AS1_ENST00000590743.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.D16823Y|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.D10326Y|TTN_ENST00000589042.1_Missense_Mutation_p.D19391Y|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.D10518Y|TTN_ENST00000359218.5_Missense_Mutation_p.D10451Y|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin			1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)		TCTCTGAAGTCGAGGTGAAGC	0.403000																								0							SO:0001583	missense			ENST00000591111.1	1	0	hg19		.	.	.	.	.	.	.	.	.	.	C	13.75	2.331152	0.41297	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.66815	-0.23;0.03;0.01;-0.01	6.17	5.3	0.74995	Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.80336	0.4604	M	0.73217	2.22	0.58432	D	0.999994	D;D;D;D	0.67145	0.996;0.996;0.996;0.996	D;D;D;D	0.68353	0.957;0.957;0.957;0.957	T	0.82926	-0.0215	9	0.87932	D	0	.	15.336	0.74255	0.0:0.9338:0.0:0.0662	.	10326;10451;10518;17750	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	Y	16823;10326;10518;10451;10324	ENSP00000343764:D16823Y;ENSP00000434586:D10326Y;ENSP00000340554:D10518Y;ENSP00000352154:D10451Y	ENSP00000340554:D10518Y	D	-	1	0	TTN	179167195	1.000000	0.71417	0.935000	0.37517	0.985000	0.73830	4.910000	0.63321	1.630000	0.50440	0.655000	0.94253	GAC		TCGA-YB-A89D-01A-12D-A36O-08	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	1	0	0	13	274	0	70		0	0	0	0	70	2		0	0	0	0	0	2	1	0.999489	13	267	0	70	2		0	0	0	0	70	2	-14.523590	1	1	0	0		1	2	2	4	2.076171	0	0.240000	3.280000	0.367510	0.490000	0.260000	1.000000	0.440000	0.547268	0.490000	0	3.600000e-01	7.200000e-01
ZC3H15	55854	broad.mit.edu	37	2	187370558	187370558	+	Missense_Mutation	SNP	G	G	T			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08			G	T	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr2:187370558G>T	ENST00000337859.6	+	8	1183	c.956G>T	c.(955-957)gGt>gTt	p.G319V	ZC3H15_ENST00000544130.1_Missense_Mutation_p.G114V	NM_018471.2	NP_060941.2	Q8WU90	ZC3HF_HUMAN	zinc finger CCCH-type containing 15			15			OV - Ovarian serous cystadenocarcinoma(117;0.0148)|Epithelial(96;0.0922)|all cancers(119;0.233)		CAGGGAACAGGTGGTGATGAG	0.428000																								0							SO:0001583	missense			ENST00000337859.6	1	1	hg19	CCDS42791.1	.	.	.	.	.	.	.	.	.	.	G	12.75	2.032400	0.35893	.	.	ENSG00000065548	ENST00000337859;ENST00000544130;ENST00000536434	T	0.29917	1.55	5.87	5.87	0.94306	.	0.478557	0.25823	N	0.028075	T	0.21022	0.0506	N	0.22421	0.69	0.50632	D	0.999884	B	0.33583	0.418	B	0.32393	0.145	T	0.04635	-1.0937	10	0.22706	T	0.39	-16.981	13.7487	0.62894	0.0701:0.0:0.9299:0.0	.	319	Q8WU90	ZC3HF_HUMAN	V	319;114;319	ENSP00000338788:G319V	ENSP00000338788:G319V	G	+	2	0	ZC3H15	187078803	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.103000	0.64578	2.941000	0.99782	0.655000	0.94253	GGT		TCGA-YB-A89D-01A-12D-A36O-08	ZC3H15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334547.2	1	0	1	14	181	0	34	1	9.993094e-01	25	139	0	34	2		0	0	0	0	0	2	1	0.999773	14	179	0	33	2		0	0	0	0	34	2	-18.426220	1	0	0	0		1	2	2	4	2.076171	0	0.240000	3.280000	0.367510	0.770000	0.430000	1.000000	1.000000	0.776428	0.770000	0	5.700000e-01	1
NDUFS1	4719	broad.mit.edu	37	2	207017231	207017231	+	Missense_Mutation	SNP	C	C	A			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr2:207017231C>A	ENST00000233190.6	-	3	331	c.65G>T	c.(64-66)cGa>cTa	p.R22L	NDUFS1_ENST00000455934.2_Missense_Mutation_p.R36L|NDUFS1_ENST00000449699.1_Missense_Mutation_p.R22L|NDUFS1_ENST00000432169.1_Intron|NDUFS1_ENST00000423725.1_Intron|NDUFS1_ENST00000440274.1_Missense_Mutation_p.R22L|NDUFS1_ENST00000457011.1_Intron	NM_005006.6	NP_004997.4	P28331	NDUS1_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 1, 75kDa (NADH-coenzyme Q reductase)			38					GGCAGTTGTTCGAACTGACCA	0.388000																								0							SO:0001583	missense			ENST00000233190.6	1	0	hg19	CCDS2366.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.048404	0.75846	.	.	ENSG00000023228	ENST00000233190;ENST00000440274;ENST00000455934;ENST00000449699;ENST00000454195	D;D;D;D;T	0.89050	-2.33;-2.46;-2.34;-2.33;-1.2	5.9	5.9	0.94986	.	0.318441	0.28332	N	0.015736	D	0.89884	0.6844	M	0.70595	2.14	0.80722	D	1	B;B;B	0.27068	0.167;0.002;0.167	B;B;B	0.28991	0.097;0.003;0.049	D	0.86939	0.2078	10	0.59425	D	0.04	.	20.2723	0.98479	0.0:1.0:0.0:0.0	.	22;36;22	E7ENF3;B4DJA0;P28331	.;.;NDUS1_HUMAN	L	22;22;36;22;22	ENSP00000233190:R22L;ENSP00000409766:R22L;ENSP00000392709:R36L;ENSP00000399912:R22L;ENSP00000389413:R22L	ENSP00000233190:R22L	R	-	2	0	NDUFS1	206725476	1.000000	0.71417	0.999000	0.59377	0.839000	0.47603	6.841000	0.75374	2.793000	0.96121	0.563000	0.77884	CGA		TCGA-YB-A89D-01A-12D-A36O-08	NDUFS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256391.4	1	0	0	16	387	0	68	0	4.010641e-01	0	33	0	68	2		0	0	0	0	0	2	1	0.999931	15	384	0	68	2		0	0	0	0	68	2	-2.746096	1	1	0	0		1	2	2	4	2.076171	0	0.240000	3.280000	0.367510	0.420000	0.240000	1.000000	0.400000	0.491640	0.420000	0	3.200000e-01	6.100000e-01
DOCK10	55619	broad.mit.edu	37	2	225729339	225729339	+	Silent	SNP	G	G	T			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr2:225729339G>T	ENST00000258390.7	-	13	1600	c.1533C>A	c.(1531-1533)atC>atA	p.I511I	DOCK10_ENST00000409592.3_Silent_p.I505I	NM_014689.2	NP_055504.2	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10			87		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)			AGACTTTTTCGATTTTGGCCA	0.363000																								0							SO:0001819	synonymous_variant			ENST00000258390.7	1	0	hg19	CCDS46528.1																																																																																				TCGA-YB-A89D-01A-12D-A36O-08	DOCK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331246.1	1	0	0	12	281	0	59	0	1.870076e-02	0	5	0	59	2		0	0	0	0	0	2	1	0.999095	12	277	0	59	2		0	0	0	0	59	2	-3.263699	1	1	0	0		1	2	2	4	2.076171	0	0.240000	3.280000	0.367510	0.440000	0.230000	1.000000	0.410000	0.509260	0.440000	0	3.200000e-01	6.700000e-01
GPR35	2859	broad.mit.edu	37	2	241569512	241569512	+	Missense_Mutation	SNP	G	G	A			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr2:241569512G>A	ENST00000319838.5	+	6	1085	c.143G>A	c.(142-144)cGc>cAc	p.R48H	GPR35_ENST00000407714.1_Missense_Mutation_p.R48H|GPR35_ENST00000430267.1_Missense_Mutation_p.R48H|GPR35_ENST00000438013.2_Missense_Mutation_p.R79H|GPR35_ENST00000403859.1_Missense_Mutation_p.R48H	NM_001195381.1	NP_001182310.1	Q9HC97	GPR35_HUMAN	G protein-coupled receptor 35			17		all_epithelial(40;7.49e-12)|Breast(86;0.000148)|Renal(207;0.00571)|Ovarian(221;0.104)|all_neural(83;0.107)|all_hematologic(139;0.182)|all_lung(227;0.186)|Melanoma(123;0.238)			TTCTGCTGCCGCATGCAGCAG	0.647000																								0							SO:0001583	missense			ENST00000319838.5	0	1	hg19	CCDS2541.1	.	.	.	.	.	.	.	.	.	.	G	16.79	3.219555	0.58560	2.27E-4	0.0	ENSG00000178623	ENST00000319838;ENST00000403859;ENST00000438013;ENST00000407714;ENST00000430267	T;T;T;T;T	0.71934	-0.61;-0.61;-0.61;-0.61;-0.61	3.81	2.92	0.33932	GPCR, rhodopsin-like superfamily (1);	0.567532	0.16439	U	0.214392	T	0.73225	0.3560	L	0.39514	1.22	0.34064	D	0.657654	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.77004	0.987;0.989;0.989	T	0.74497	-0.3646	10	0.36615	T	0.2	-28.6438	6.1563	0.20340	0.2348:0.0:0.7652:0.0	.	133;79;48	Q6ZMP9;A8K2J1;Q9HC97	.;.;GPR35_HUMAN	H	48;48;79;48;48	ENSP00000322731:R48H;ENSP00000385140:R48H;ENSP00000415890:R79H;ENSP00000384263:R48H;ENSP00000411788:R48H	ENSP00000322731:R48H	R	+	2	0	GPR35	241218185	0.000000	0.05858	0.789000	0.31954	0.616000	0.37450	-0.018000	0.12568	0.937000	0.37394	0.462000	0.41574	CGC		TCGA-YB-A89D-01A-12D-A36O-08	GPR35-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000325631.1	0	0	0	6	250	0	67	0	8.443615e-01	0	142	0	67	2		0	0	0	0	0	2	1	0.963305	6	245	0	66	2		0	0	0	0	67	2	-3.145491	1	1	121406	3	36	1	2	2	4	2.076171	0	0.240000	3.280000	0.367510	0.270000	0.100000	1.000000	0.220000	0.361673	0.270000	0	1.700000e-01	4.700000e-01
HDLBP	3069	broad.mit.edu	37	2	242194513	242194513	+	Missense_Mutation	SNP	C	C	A			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr2:242194513C>A	ENST00000391975.1	-	9	1368	c.1141G>T	c.(1141-1143)Ggc>Tgc	p.G381C	HDLBP_ENST00000427183.2_Missense_Mutation_p.G348C|HDLBP_ENST00000310931.4_Missense_Mutation_p.G381C|HDLBP_ENST00000391976.2_Missense_Mutation_p.G381C	NM_203346.3	NP_976221	Q00341	VIGLN_HUMAN	high density lipoprotein binding protein			44		all_cancers(19;7.77e-41)|all_epithelial(40;1.74e-18)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00338)|Ovarian(221;0.00556)|Lung NSC(271;0.0121)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)			CCTTTCTTGCCAATGATGAAA	0.478000																								0							SO:0001583	missense			ENST00000391975.1	0	1	hg19	CCDS2547.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	34|34|34	5.374320|5.374320|5.374320	0.95923|0.95923|0.95923	.|.|.	.|.|.	ENSG00000115677|ENSG00000115677|ENSG00000115677	ENST00000391975;ENST00000391976;ENST00000310931;ENST00000427183|ENST00000453141|ENST00000373292	D;D;D;D|.|.	0.88741|.|.	-2.42;-2.42;-2.42;-2.42|.|.	5.93|5.93|5.93	5.93|5.93|5.93	0.95920|0.95920|0.95920	K Homology (1);K Homology, type 1, subgroup (1);K Homology, type 1 (1);|.|.	0.000000|.|.	0.85682|.|.	D|.|.	0.000000|.|.	D|D|D	0.84543|0.84543|0.84543	0.5495|0.5495|0.5495	M|M|M	0.86651|0.86651|0.86651	2.83|2.83|2.83	0.80722|0.80722|0.80722	D|D|D	1|1|1	D;D;D|.|.	0.89917|.|.	1.0;1.0;1.0|.|.	D;D;D|.|.	0.97110|.|.	1.0;1.0;1.0|.|.	D|D|D	0.85095|0.85095|0.85095	0.0954|0.0954|0.0954	10|5|5	0.87932|.|.	D|.|.	0|.|.	-37.045|-37.045|-37.045	20.3539|20.3539|20.3539	0.98825|0.98825|0.98825	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.|.	381;348;381|.|.	B2R5V9;E7EM71;Q00341|.|.	.;.;VIGLN_HUMAN|.|.	C|F|L	381;381;381;348|258|189	ENSP00000375836:G381C;ENSP00000375837:G381C;ENSP00000312042:G381C;ENSP00000399139:G348C|.|.	ENSP00000312042:G381C|.|.	G|L|W	-|-|-	1|3|2	0|2|0	HDLBP|HDLBP|HDLBP	241843186|241843186|241843186	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	0.997000|0.997000|0.997000	0.53966|0.53966|0.53966	0.963000|0.963000|0.963000	0.63663|0.63663|0.63663	7.755000|7.755000|7.755000	0.85180|0.85180|0.85180	2.826000|2.826000|2.826000	0.97356|0.97356|0.97356	0.655000|0.655000|0.655000	0.94253|0.94253|0.94253	GGC|TTG|TGG		TCGA-YB-A89D-01A-12D-A36O-08	HDLBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257245.5	0	0	0	12	1228	0	250	0	8.645303e-01	0	366	0	250	2		0	0	0	0	0	2	1	0.999022	14	1208	0	246	2		0	0	0	0	250	2	-2.063559	0	1	0	0		1	2	2	4	2.076171	0	0.240000	3.280000	0.367510	0.100000	0.040000	1.000000	0.110000	0.217152	0.100000	0	6.000000e-02	1.700000e-01
TCF23	150921	broad.mit.edu	37	2	27373013	27373013	+	Missense_Mutation	SNP	C	C	T			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr2:27373013C>T	ENST00000296096.5	+	2	375	c.245C>T	c.(244-246)gCc>gTc	p.A82V		NM_175769.2	NP_786951.1	Q7RTU1	TCF23_HUMAN	transcription factor 23			14	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				CCTGAGAATGCCGCGCGGGAG	0.652000																								0							SO:0001583	missense			ENST00000296096.5	0	1	hg19	CCDS33163.1	.	.	.	.	.	.	.	.	.	.	C	33	5.221376	0.95139	.	.	ENSG00000163792	ENST00000296096	D	0.97906	-4.6	5.66	5.66	0.87406	Helix-loop-helix DNA-binding (5);	0.054766	0.64402	D	0.000001	D	0.98150	0.9389	M	0.65975	2.015	0.53688	D	0.999972	D	0.60160	0.987	P	0.60789	0.879	D	0.98239	1.0487	10	0.48119	T	0.1	-6.4656	17.2403	0.87011	0.0:1.0:0.0:0.0	.	82	Q7RTU1	TCF23_HUMAN	V	82	ENSP00000296096:A82V	ENSP00000296096:A82V	A	+	2	0	TCF23	27226517	1.000000	0.71417	0.879000	0.34478	0.676000	0.39594	5.750000	0.68712	2.680000	0.91292	0.561000	0.74099	GCC		TCGA-YB-A89D-01A-12D-A36O-08	TCF23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324980.1	0	0	0	5	264	0	54	0	1.675961e-03	0	3	0	54	2		0	0	0	0	0	2	1	0.936888	6	261	0	53	2		0	0	0	0	54	2	-2.900013	1	1	0	0		1	2	2	4	2.171355	1	0.240000	3.280000	0.387097	0.200000	0.070000	0.420000	0.200000	0.227449	0.200000	0	1.300000e-01	3.100000e-01
CCDC88A	55704	broad.mit.edu	37	2	55570840	55570840	+	Nonsense_Mutation	SNP	G	G	T			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr2:55570840G>T	ENST00000436346.1	-	12	2118	c.1277C>A	c.(1276-1278)tCa>tAa	p.S426*	AC012358.8_ENST00000594078.1_RNA|CCDC88A_ENST00000263630.8_Nonsense_Mutation_p.S426*|CCDC88A_ENST00000336838.6_Nonsense_Mutation_p.S426*|CCDC88A_ENST00000413716.2_Nonsense_Mutation_p.S426*	NM_001135597.1|NM_001254943.1	NP_001129069.1|NP_001241872.1	Q3V6T2	GRDN_HUMAN	coiled-coil domain containing 88A			69					AAGATGTAATGATTCATCCAT	0.318000																								0							SO:0001587	stop_gained			ENST00000436346.1	0	1	hg19		.	.	.	.	.	.	.	.	.	.	G	40	8.219217	0.98712	.	.	ENSG00000115355	ENST00000336838;ENST00000263630;ENST00000436346;ENST00000413716	.	.	.	5.91	5.91	0.95273	.	0.000000	0.39475	U	0.001343	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.3066	20.3011	0.98612	0.0:0.0:1.0:0.0	.	.	.	.	X	426	.	ENSP00000263630:S426X	S	-	2	0	CCDC88A	55424344	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.378000	0.97191	2.804000	0.96469	0.650000	0.86243	TCA		TCGA-YB-A89D-01A-12D-A36O-08	CCDC88A-203	KNOWN	basic	protein_coding	protein_coding		0	0	0	12	503	1	83	0	3.145949e-02	0	11	1	83	2		0	0	0	0	0	2	0	0.096119	12	496	1	81	20		0	0	0	1	83	2	-2.823380	1	1	0	0		1	2	2	4	2.171355	1	0.240000	3.280000	0.387097	0.240000	0.120000	0.400000	0.240000	0.259040	0.240000	0	1.800000e-01	3.300000e-01
CNRIP1	25927	broad.mit.edu	37	2	68544303	68544303	+	Nonsense_Mutation	SNP	G	G	A			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr2:68544303G>A	ENST00000263655.3	-	2	921	c.316C>T	c.(316-318)Cag>Tag	p.Q106*	CNRIP1_ENST00000481714.1_5'UTR|CNRIP1_ENST00000409862.1_Nonsense_Mutation_p.Q106*|CNRIP1_ENST00000409559.3_Nonsense_Mutation_p.Q106*	NM_015463.2	NP_056278.1	Q96F85	CNRP1_HUMAN	cannabinoid receptor interacting protein 1			9					ATGGTGATCTGGATGGGTTGC	0.468000																								0							SO:0001587	stop_gained			ENST00000263655.3	0	1	hg19	CCDS1886.1	.	.	.	.	.	.	.	.	.	.	G	37	6.464642	0.97590	.	.	ENSG00000119865	ENST00000409559;ENST00000263655;ENST00000409862	.	.	.	5.16	5.16	0.70880	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.48119	T	0.1	-13.3606	17.0178	0.86424	0.0:0.0:1.0:0.0	.	.	.	.	X	106	.	ENSP00000263655:Q106X	Q	-	1	0	CNRIP1	68397807	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.967000	0.93402	2.697000	0.92050	0.555000	0.69702	CAG		TCGA-YB-A89D-01A-12D-A36O-08	CNRIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251758.1	0	0	0	9	854	1	179	0	4.221386e-02	0	63	1	179	3		0	0	0	0	0	2	0	0.075600	11	837	1	177	17		0	0	0	1	179	2	-2.458060	0	1	0	0		1	2	2	4	2.171355	1	0.240000	3.280000	0.387097	0.110000	0.040000	0.200000	0.120000	0.119310	0.110000	0	7.000000e-02	1.600000e-01
DYSF	8291	broad.mit.edu	37	2	71891480	71891480	+	Nonsense_Mutation	SNP	G	G	T			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr2:71891480G>T	ENST00000258104.3	+	45	5246	c.4969G>T	c.(4969-4971)Gaa>Taa	p.E1657*	DYSF_ENST00000429174.2_Nonsense_Mutation_p.E1678*|DYSF_ENST00000410020.3_Nonsense_Mutation_p.E1696*|DYSF_ENST00000479049.2_3'UTR|DYSF_ENST00000413539.2_Nonsense_Mutation_p.E1688*|DYSF_ENST00000409762.1_Nonsense_Mutation_p.E1674*|DYSF_ENST00000409651.1_Nonsense_Mutation_p.E1689*|DYSF_ENST00000409744.1_Nonsense_Mutation_p.E1665*|DYSF_ENST00000409582.3_Nonsense_Mutation_p.E1695*|DYSF_ENST00000409366.1_Nonsense_Mutation_p.E1679*|DYSF_ENST00000394120.2_Nonsense_Mutation_p.E1658*|DYSF_ENST00000410041.1_Nonsense_Mutation_p.E1675*	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin			111					CTCCAAGGACGAAAAGATCGG	0.552000																								0		GRCh37	CM070072	DYSF	M		SO:0001587	stop_gained			ENST00000258104.3	0	1	hg19	CCDS1918.1	.	.	.	.	.	.	.	.	.	.	G	48	13.931724	0.99771	.	.	ENSG00000135636	ENST00000413539;ENST00000409762;ENST00000409582;ENST00000429174;ENST00000258104;ENST00000409651;ENST00000394120;ENST00000409744;ENST00000409366;ENST00000410020;ENST00000410041	.	.	.	5.13	5.13	0.70059	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-19.6304	16.0724	0.80943	0.0:0.0:1.0:0.0	.	.	.	.	X	1688;1674;1695;1678;1657;1689;1658;1665;1679;1696;1675	.	ENSP00000258104:E1657X	E	+	1	0	DYSF	71744988	1.000000	0.71417	0.932000	0.37286	0.935000	0.57460	7.864000	0.87037	2.393000	0.81446	0.561000	0.74099	GAA		TCGA-YB-A89D-01A-12D-A36O-08	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	0	0	0	9	442	0	80	0	1.298296e-01	0	28	0	80	2		0	0	0	0	0	2	1	0.993770	9	434	0	80	2		0	0	0	0	80	2	-3.152065	1	1	0	0		1	2	2	4	2.171355	1	0.240000	3.280000	0.387097	0.210000	0.090000	0.370000	0.200000	0.227314	0.210000	0	1.500000e-01	3.000000e-01
NAT8	9027	broad.mit.edu	37	2	73868603	73868603	+	Silent	SNP	G	G	A			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr2:73868603G>A	ENST00000272425.3	-	2	302	c.153C>T	c.(151-153)ctC>ctT	p.L51L		NM_003960.3|NM_016347.2	NP_003951.3|NP_057431.2			N-acetyltransferase 8 (GCN5-related, putative)	p.L51L(1)		9					GGAGTAGGGCGAGGGGCCCCC	0.612000																								1	Substitution - coding silent(1)						SO:0001819	synonymous_variant			ENST00000272425.3	0	1	hg19	CCDS1926.1																																																																																				TCGA-YB-A89D-01A-12D-A36O-08	NAT8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327854.1	0	0	0	7	558	0	127		0	0	0	0	127	2		0	0	0	0	0	2	1	0.979572	7	549	0	124	2		0	0	0	0	127	2	-2.920183	1	1	121410	3	37	1	2	2	4	2.171355	1	0.240000	3.280000	0.387097	0.130000	0.050000	0.250000	0.120000	0.145429	0.130000	0	8.000000e-02	2.000000e-01
TMEM131	23505	broad.mit.edu	37	2	98422018	98422018	+	Nonsense_Mutation	SNP	G	G	T			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr2:98422018G>T	ENST00000186436.5	-	20	2432	c.2204C>A	c.(2203-2205)tCa>tAa	p.S735*		NM_015348.1	NP_056163.1	Q92545	TM131_HUMAN	transmembrane protein 131			57					TCAAACCTTTGATTTTTTTCC	0.358000																								0							SO:0001587	stop_gained			ENST00000186436.5	0	1	hg19	CCDS46368.1	.	.	.	.	.	.	.	.	.	.	G	42	9.342510	0.99142	.	.	ENSG00000075568	ENST00000186436	.	.	.	6.07	6.07	0.98685	.	0.120296	0.64402	D	0.000018	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-17.5958	20.6593	0.99626	0.0:0.0:1.0:0.0	.	.	.	.	X	735	.	ENSP00000186436:S735X	S	-	2	0	TMEM131	97788450	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	9.476000	0.97823	2.885000	0.99019	0.655000	0.94253	TCA		TCGA-YB-A89D-01A-12D-A36O-08	TMEM131-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329285.2	0	0	0	29	983	0	201	0	3.405676e-01	0	41	0	201	2		0	0	0	0	0	2	1	1.000000	30	966	0	197	2		0	0	0	0	201	2	-2.633335	1	1	0	0		1	2	2	4	2.171355	1	0.240000	3.280000	0.387097	0.290000	0.190000	0.420000	0.290000	0.305248	0.290000	0	2.400000e-01	3.600000e-01
COL6A5	256076	broad.mit.edu	37	3	130174477	130174477	+	Missense_Mutation	SNP	C	C	A			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr3:130174477C>A	ENST00000432398.2	+	37	7251	c.6757C>A	c.(6757-6759)Caa>Aaa	p.Q2253K	COL6A5_ENST00000265379.6_Missense_Mutation_p.Q2253K	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	p.Q292K(1)|p.Q2253K(1)		44					TGAAAAAGATCAAAAATCTGC	0.333000																								2	Substitution - Missense(2)						SO:0001583	missense			ENST00000432398.2	0	1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	3.821|3.821	-0.037685|-0.037685	0.07497|0.07497	.|.	.|.	ENSG00000172752|ENSG00000172752	ENST00000432398;ENST00000265379;ENST00000373157;ENST00000512482|ENST00000512836	D;D;T;T|.	0.88818|.	-2.34;-2.43;-0.87;-0.75|.	4.26|4.26	0.026|0.026	0.14148|0.14148	.|.	2.119150|.	0.02670|.	N|.	0.108475|.	T|.	0.21841|.	0.0526|.	N|N	0.17474|0.17474	0.49|0.49	0.09310|0.09310	N|N	1|1	B;B|.	0.02656|.	0.0;0.0|.	B;B|.	0.04013|.	0.0;0.001|.	T|.	0.30031|.	-0.9992|.	10|.	0.02654|.	T|.	1|.	.|.	8.2937|8.2937	0.31973|0.31973	0.3027:0.5542:0.1431:0.0|0.3027:0.5542:0.1431:0.0	.|.	2253;2253|.	A8TX70;A8TX70-2|.	CO6A5_HUMAN;.|.	K|X	2253;2253;196;88|504	ENSP00000390895:Q2253K;ENSP00000265379:Q2253K;ENSP00000362250:Q196K;ENSP00000424968:Q88K|.	ENSP00000265379:Q2253K|.	Q|S	+|+	1|2	0|0	COL6A5|COL6A5	131657167|131657167	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	-0.464000|-0.464000	0.06688|0.06688	0.170000|0.170000	0.19704|0.19704	-0.846000|-0.846000	0.03041|0.03041	CAA|TCA		TCGA-YB-A89D-01A-12D-A36O-08	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		0	0	0	8	321	0	52	0	0	0	1	0	52	2		0	0	0	0	0	2	1	0.989055	7	318	0	51	2		0	0	0	0	52	2	-8.123208	1	0	0	0		1	1	2	3	1.937366	0	0.240000	3.280000	0.321429	0.230000	0.100000	0.420000	0.220000	0.252148	0.230000	0	1.600000e-01	3.300000e-01
PLCH1	23007	broad.mit.edu	37	3	155241698	155241698	+	Missense_Mutation	SNP	G	G	T			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr3:155241698G>T	ENST00000340059.7	-	10	1421	c.1422C>A	c.(1420-1422)ttC>ttA	p.F474L	PLCH1_ENST00000460012.1_Missense_Mutation_p.F456L|PLCH1_ENST00000414191.1_Missense_Mutation_p.F456L|PLCH1_ENST00000447496.2_Missense_Mutation_p.F474L|PLCH1_ENST00000334686.6_Missense_Mutation_p.F456L|PLCH1_ENST00000494598.1_Missense_Mutation_p.F474L	NM_001130960.1	NP_001124432.1	Q4KWH8	PLCH1_HUMAN	phospholipase C, eta 1			107			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)		AATGGAGCTTGAATTTGCACT	0.423000																								0							SO:0001583	missense			ENST00000340059.7	0	1	hg19	CCDS46939.1	.	.	.	.	.	.	.	.	.	.	G	6.629	0.484579	0.12641	.	.	ENSG00000114805	ENST00000494598;ENST00000460012;ENST00000447496;ENST00000340059;ENST00000334686;ENST00000414191	T;T;T;T;T;T	0.35236	1.32;1.32;1.32;1.32;1.32;1.32	5.48	-0.01	0.13998	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (1);	0.215323	0.44483	D	0.000450	T	0.10551	0.0258	N	0.04018	-0.295	0.36115	D	0.845089	B;B;B	0.06786	0.001;0.001;0.0	B;B;B	0.12837	0.008;0.003;0.001	T	0.32929	-0.9888	10	0.02654	T	1	.	2.8455	0.05541	0.3453:0.0932:0.4209:0.1405	.	456;474;474	Q4KWH8-2;Q4KWH8;Q4KWH8-3	.;PLCH1_HUMAN;.	L	474;456;474;474;456;456	ENSP00000419100:F474L;ENSP00000417502:F456L;ENSP00000402759:F474L;ENSP00000345988:F474L;ENSP00000335469:F456L;ENSP00000412977:F456L	ENSP00000335469:F456L	F	-	3	2	PLCH1	156724392	0.992000	0.36948	0.998000	0.56505	0.985000	0.73830	0.126000	0.15769	0.036000	0.15547	0.563000	0.77884	TTC		TCGA-YB-A89D-01A-12D-A36O-08	PLCH1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351125.1	0	0	0	13	616	0	149	0	3.054130e-03	0	4	0	149	2		0	0	0	0	0	2	1	0.999512	13	611	0	148	2		0	0	0	0	149	2	-2.761894	1	1	0	0		1	1	2	3	1.940373	0	0.240000	3.280000	0.321429	0.190000	0.100000	0.320000	0.190000	0.206379	0.190000	0	1.400000e-01	2.600000e-01
ECT2	1894	broad.mit.edu	37	3	172473162	172473162	+	Missense_Mutation	SNP	A	A	C			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr3:172473162A>C	ENST00000392692.3	+	3	384	c.208A>C	c.(208-210)Aag>Cag	p.K70Q	ECT2_ENST00000417960.1_Missense_Mutation_p.K69Q|ECT2_ENST00000232458.5_Missense_Mutation_p.K70Q|ECT2_ENST00000427830.1_Missense_Mutation_p.K70Q|ECT2_ENST00000441497.2_Missense_Mutation_p.K70Q|ECT2_ENST00000540509.1_Missense_Mutation_p.K70Q	NM_001258315.1	NP_001245244.1	Q9H8V3	ECT2_HUMAN	epithelial cell transforming 2			37	Ovarian(172;0.00197)|Breast(254;0.158)		Lung(28;1.33e-14)|LUSC - Lung squamous cell carcinoma(14;1.48e-14)		AAAAGCCTTAAAGGTACGGAG	0.313000																								0							SO:0001583	missense			ENST00000392692.3	1	1	hg19	CCDS58860.1	.	.	.	.	.	.	.	.	.	.	A	5.267	0.234752	0.09969	.	.	ENSG00000114346	ENST00000232458;ENST00000392692;ENST00000427830;ENST00000417960;ENST00000428567;ENST00000426894;ENST00000366090;ENST00000415665;ENST00000438041;ENST00000441497;ENST00000540509	T;T;T;T;T;T;T;T;T;T;T	0.66099	-0.02;-0.19;-0.04;-0.02;0.97;0.93;0.87;1.01;0.87;-0.02;-0.19	5.58	3.14	0.36123	.	0.162995	0.56097	N	0.000021	T	0.31949	0.0813	N	0.11560	0.145	0.32649	N	0.51964	B;B;B;B	0.16166	0.005;0.015;0.001;0.016	B;B;B;B	0.20184	0.008;0.028;0.011;0.006	T	0.34576	-0.9823	10	0.02654	T	1	-6.7187	3.8864	0.09100	0.5385:0.1802:0.2813:0.0	.	70;70;70;69	Q9H8V3;Q9H8V3-3;G5E9L8;Q9H8V3-2	ECT2_HUMAN;.;.;.	Q	70;70;70;69;69;70;70;70;70;70;70	ENSP00000232458:K70Q;ENSP00000376457:K70Q;ENSP00000401910:K70Q;ENSP00000415876:K69Q;ENSP00000403501:K69Q;ENSP00000412331:K70Q;ENSP00000403446:K70Q;ENSP00000412028:K70Q;ENSP00000389108:K70Q;ENSP00000412259:K70Q;ENSP00000443160:K70Q	ENSP00000232458:K70Q	K	+	1	0	ECT2	173955856	1.000000	0.71417	1.000000	0.80357	0.859000	0.49053	1.277000	0.33167	0.384000	0.24942	0.402000	0.26972	AAG		TCGA-YB-A89D-01A-12D-A36O-08	ECT2-003	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000345994.2	1	0	1	28	236	0	35	0	3.805722e-01	0	12	0	35	2		0	0	0	0	0	2	1	1.000000	28	234	0	35	2		0	0	0	0	35	2	-20.000000	1	1	0	0		1	1	2	3	1.940373	0	0.240000	3.280000	0.321429	0.990000	0.680000	1.000000	1.000000	0.934345	0.990000	1	8.200000e-01	1
KCNH8	131096	broad.mit.edu	37	3	19431991	19431991	+	Missense_Mutation	SNP	G	G	T			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr3:19431991G>T	ENST00000328405.2	+	6	1096	c.830G>T	c.(829-831)cGa>cTa	p.R277L	KCNH8_ENST00000475063.1_3'UTR|KCNH8_ENST00000537696.1_5'Flank	NM_144633.2	NP_653234.2	Q96L42	KCNH8_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 8			77					TTAAATTTCCGAACAACTTAT	0.358000													NSCLC(124;1625 1765 8018 24930 42026)											0							SO:0001583	missense			ENST00000328405.2	1	0	hg19	CCDS2632.1	.	.	.	.	.	.	.	.	.	.	G	33	5.217758	0.95104	.	.	ENSG00000183960	ENST00000328405	D	0.98178	-4.77	5.78	5.78	0.91487	Ion transport (1);	0.000000	0.27027	U	0.021300	D	0.98651	0.9548	L	0.60012	1.86	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.98974	1.0802	9	.	.	.	.	20.0085	0.97443	0.0:0.0:1.0:0.0	.	277;277	B7Z398;Q96L42	.;KCNH8_HUMAN	L	277	ENSP00000328813:R277L	.	R	+	2	0	KCNH8	19406995	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.869000	0.99810	2.723000	0.93209	0.650000	0.86243	CGA		TCGA-YB-A89D-01A-12D-A36O-08	KCNH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252139.2	1	0	0	17	499	0	124	0	0	0	1	0	124	2		0	0	0	0	0	2	1	0.999960	16	490	0	122	2		0	0	0	0	124	2	-2.955643	1	1	0	0		1	1	2	3	1.907330	0	0.240000	3.280000	0.321429	0.310000	0.180000	0.470000	0.300000	0.322996	0.310000	0	2.400000e-01	3.900000e-01
NGLY1	55768	broad.mit.edu	37	3	25770651	25770651	+	Missense_Mutation	SNP	G	G	T			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr3:25770651G>T	ENST00000280700.5	-	10	1744	c.1584C>A	c.(1582-1584)ttC>ttA	p.F528L	NGLY1_ENST00000428257.1_Missense_Mutation_p.F510L|NGLY1_ENST00000422724.2_3'UTR|NGLY1_ENST00000467224.1_5'UTR|NGLY1_ENST00000396649.3_Missense_Mutation_p.F528L|NGLY1_ENST00000417874.2_Missense_Mutation_p.F486L	NM_018297.3	NP_060767.2	Q96IV0	NGLY1_HUMAN	N-glycanase 1			18					CAACTTTTCTGAATATAGATT	0.313000																								0							SO:0001583	missense			ENST00000280700.5	1	1	hg19	CCDS33719.1	.	.	.	.	.	.	.	.	.	.	G	19.60	3.857742	0.71834	.	.	ENSG00000151092	ENST00000428257;ENST00000280700;ENST00000396649;ENST00000308710;ENST00000417874	D;D;D;D	0.95918	-3.85;-3.85;-3.85;-3.85	5.82	4.0	0.46444	Peptide N glycanase, PAW domain (3);Galactose-binding domain-like (1);	0.199148	0.53938	D	0.000042	D	0.96706	0.8925	M	0.82193	2.58	0.80722	D	1	D;D;P;D	0.69078	0.997;0.966;0.937;0.993	P;P;P;P	0.61397	0.888;0.466;0.814;0.618	D	0.96101	0.9069	10	0.59425	D	0.04	-7.2391	7.6939	0.28583	0.1442:0.3228:0.533:0.0	.	486;510;528;528	B4DJE9;Q96IV0-2;Q96IV0-3;Q96IV0	.;.;.;NGLY1_HUMAN	L	510;528;528;507;486	ENSP00000387430:F510L;ENSP00000280700:F528L;ENSP00000307980:F507L;ENSP00000389888:F486L	ENSP00000280700:F528L	F	-	3	2	NGLY1	25745655	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.762000	0.47597	1.439000	0.47511	0.561000	0.74099	TTC		TCGA-YB-A89D-01A-12D-A36O-08	NGLY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340832.2	0	0	0	22	686	0	137	0	4.959406e-01	1	51	0	137	2		0	0	0	0	0	2	1	0.999998	20	669	0	134	2		0	0	0	0	137	2	-2.982957	1	1	0	0		1	1	2	3	1.907330	0	0.240000	3.280000	0.321429	0.290000	0.180000	0.420000	0.300000	0.301443	0.290000	0	2.300000e-01	3.600000e-01
PTPRG	5793	broad.mit.edu	37	3	62268492	62268492	+	Missense_Mutation	SNP	G	G	A			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr3:62268492G>A	ENST00000474889.1	+	28	4380	c.4003G>A	c.(4003-4005)Gtc>Atc	p.V1335I	PTPRG_ENST00000295874.10_Missense_Mutation_p.V1306I|PTPRG-AS1_ENST00000495542.1_RNA|PTPRG-AS1_ENST00000462497.1_RNA|PTPRG-AS1_ENST00000490916.1_RNA|PTPRG-AS1_ENST00000474795.1_RNA|PTPRG-AS1_ENST00000475371.1_RNA|PTPRG-AS1_ENST00000479018.1_RNA|PTPRG-AS1_ENST00000466893.1_RNA	NM_002841.3	NP_002832.3	P23470	PTPRG_HUMAN	protein tyrosine phosphatase, receptor type, G			62					ACTTATCAACGTCATCAAGGA	0.398000																								0							SO:0001583	missense			ENST00000474889.1	1	1	hg19	CCDS2895.1	.	.	.	.	.	.	.	.	.	.	G	12.77	2.036448	0.35893	.	.	ENSG00000144724	ENST00000474889;ENST00000295874	D;D	0.83250	-1.7;-1.7	5.38	5.38	0.77491	Protein-tyrosine phosphatase, receptor/non-receptor type (3);Protein-tyrosine/Dual-specificity phosphatase (1);	0.121307	0.56097	D	0.000033	T	0.56688	0.2002	N	0.00991	-1.07	0.58432	D	0.999999	B;P;B	0.39940	0.029;0.696;0.382	B;B;B	0.30401	0.011;0.115;0.036	T	0.65717	-0.6100	10	0.13853	T	0.58	.	19.3366	0.94322	0.0:0.0:1.0:0.0	.	581;1306;1335	B7Z3T1;P23470-2;P23470	.;.;PTPRG_HUMAN	I	1335;1306	ENSP00000418112:V1335I;ENSP00000295874:V1306I	ENSP00000295874:V1306I	V	+	1	0	PTPRG	62243532	1.000000	0.71417	0.990000	0.47175	0.983000	0.72400	6.473000	0.73572	2.799000	0.96334	0.650000	0.86243	GTC		TCGA-YB-A89D-01A-12D-A36O-08	PTPRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351674.1	1	0	1	92	811	0	163	1	8.360778e-01	3	28	0	163	2		0	0	0	0	0	2	1	1.000000	91	807	0	161	2		0	0	0	0	163	2	-20.000000	1	0	0	0		1	1	2	3	1.907330	0	0.240000	3.280000	0.321429	0.940000	0.770000	1.000000	1.000000	0.936407	0.940000	1	8.500000e-01	1
ADH1A	124	broad.mit.edu	37	4	100203666	100203666	+	Missense_Mutation	SNP	G	G	A			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr4:100203666G>A	ENST00000209668.2	-	6	778	c.665C>T	c.(664-666)gCg>gTg	p.A222V	RP11-696N14.1_ENST00000500358.2_RNA|RP11-696N14.1_ENST00000506160.1_RNA	NM_000667.3	NP_000658.1	P07327	ADH1A_HUMAN	alcohol dehydrogenase 1A (class I), alpha polypeptide			25				Ethanol(DB00898)|Fomepizole(DB01213)	GATGTCCACCGCAATGATTCT	0.532000																								0							SO:0001583	missense			ENST00000209668.2	0	1	hg19	CCDS3648.1	.	.	.	.	.	.	.	.	.	.	G	11.27	1.588433	0.28357	.	.	ENSG00000187758	ENST00000209668	T	0.04970	3.52	3.11	-0.519	0.11939	Alcohol dehydrogenase, C-terminal (1);NAD(P)-binding domain (1);	0.245941	0.39146	N	0.001456	T	0.19446	0.0467	M	0.74881	2.28	0.27511	N	0.951696	P;D	0.76494	0.877;0.999	B;P	0.60541	0.175;0.876	T	0.10405	-1.0631	10	0.59425	D	0.04	-7.6741	15.9733	0.80036	0.0:0.6313:0.3687:0.0	.	13;222	B4E1R1;P07327	.;ADH1A_HUMAN	V	222	ENSP00000209668:A222V	ENSP00000209668:A222V	A	-	2	0	ADH1A	100422689	0.001000	0.12720	0.529000	0.27951	0.148000	0.21650	-0.192000	0.09587	0.061000	0.16311	0.460000	0.39030	GCG		TCGA-YB-A89D-01A-12D-A36O-08	ADH1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253669.1	0	0	0	32	1423	0	412	0	5.274485e-04	0	2	0	412	2		0	0	0	0	0	2	1	1.000000	30	1344	0	430	2		0	0	0	0	412	2	-2.256523	0	1	121412	1	35	1	2	2	4	2.119847	1	0.240000	3.280000	0.379896	0.220000	0.140000	1.000000	0.230000	0.267174	0.220000	0	1.800000e-01	2.800000e-01
CENPE	1062	broad.mit.edu	37	4	104084687	104084687	+	Silent	SNP	C	C	A			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr4:104084687C>A	ENST00000265148.3	-	17	1760	c.1671G>T	c.(1669-1671)tcG>tcT	p.S557S	CENPE_ENST00000380026.3_Intron	NM_001813.2	NP_001804.2	Q02224	CENPE_HUMAN	centromere protein E, 312kDa			101					TCTTTAAGTTCGAAATTTCAT	0.284000																								0							SO:0001819	synonymous_variant			ENST00000265148.3	1	0	hg19	CCDS34042.1																																																																																				TCGA-YB-A89D-01A-12D-A36O-08	CENPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		1	0	0	13	265	0	38		0	0	0	0	38	2		0	0	0	0	0	2	1	0.999535	13	263	0	38	2		0	0	0	0	38	2	-4.375522	1	1	121352	1	36	1	2	2	4	2.119847	1	0.240000	3.280000	0.379896	0.500000	0.270000	1.000000	0.470000	0.530738	0.500000	0	3.700000e-01	6.700000e-01
RPL34	6164	broad.mit.edu	37	4	109546320	109546320	+	Silent	SNP	C	C	A	rs143745435		TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08			C	A	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr4:109546320C>A	ENST00000394668.2	+	5	372	c.306C>A	c.(304-306)atC>atA	p.I102I	RPL34_ENST00000502534.1_Silent_p.I102I|RPL34_ENST00000394667.3_Silent_p.I102I|RPL34_ENST00000506397.1_Silent_p.I102I|RPL34_ENST00000394665.1_Silent_p.I102I	NM_033625.2	NP_296374.1	P49207	RL34_HUMAN	ribosomal protein L34			4		Hepatocellular(203;0.217)			AGCAGAAAATCGTTGTGAAAG	0.318000																								0							SO:0001819	synonymous_variant			ENST00000394668.2	1	0	hg19	CCDS3680.1																																																																																				TCGA-YB-A89D-01A-12D-A36O-08	RPL34-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363468.1	1	0	0	12	286	0	35	1	1	2	4648	0	35	2		0	0	0	0	0	2	1	0.999095	11	283	0	33	2		0	0	0	0	35	2	-3.040405	1	1	121410	1	32	1	2	2	4	2.119847	1	0.240000	3.280000	0.379896	0.430000	0.230000	1.000000	0.410000	0.466448	0.430000	0	3.100000e-01	5.900000e-01
SLIT2	9353	broad.mit.edu	37	4	20525792	20525792	+	Missense_Mutation	SNP	G	G	A			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr4:20525792G>A	ENST00000504154.1	+	14	1682	c.1430G>A	c.(1429-1431)cGt>cAt	p.R477H	SLIT2_ENST00000273739.5_Missense_Mutation_p.R481H|SLIT2_ENST00000503837.1_Missense_Mutation_p.R481H|SLIT2_ENST00000503823.1_Missense_Mutation_p.R477H	NM_004787.1	NP_004778.1	O94813	SLIT2_HUMAN	slit homolog 2 (Drosophila)			116					AAGAAATTCCGTTGTTCAGGT	0.478000																								0							SO:0001583	missense			ENST00000504154.1	1	1	hg19	CCDS3426.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	34	5.335323	0.95758	.	.	ENSG00000145147	ENST00000503823;ENST00000504154;ENST00000273739;ENST00000382173;ENST00000503837	T;T;T;T	0.81163	-1.45;-1.46;-1.37;-1.43	5.93	5.93	0.95920	Cysteine-rich flanking region, C-terminal (2);	0.000000	0.85682	D	0.000000	D	0.88097	0.6345	L	0.50919	1.6	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.76575	0.987;0.988	D	0.87886	0.2681	10	0.72032	D	0.01	.	20.3368	0.98748	0.0:0.0:1.0:0.0	.	477;477	O94813-3;O94813	.;SLIT2_HUMAN	H	477;477;481;481;481	ENSP00000427548:R477H;ENSP00000422591:R477H;ENSP00000273739:R481H;ENSP00000422261:R481H	ENSP00000273739:R481H	R	+	2	0	SLIT2	20134890	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.807000	0.99171	2.805000	0.96524	0.655000	0.94253	CGT		TCGA-YB-A89D-01A-12D-A36O-08	SLIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250396.2	1	0	0	114	398	0	100	0	9.625000e-01	0	21	0	100	2		0	0	0	0	0	2	1	1.000000	113	392	0	100	2		0	0	0	0	100	2	-20.000000	1	1	121410	3	37	1	2	2	4	2.119847	1	0.240000	3.280000	0.379896	0.990000	0.990000	1.000000	1.000000	1.000000	0.990000	1	9.900000e-01	1
GPR125	166647	broad.mit.edu	37	4	22389706	22389706	+	Silent	SNP	C	C	A			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr4:22389706C>A	ENST00000334304.5	-	19	3857	c.3588G>T	c.(3586-3588)acG>acT	p.T1196T	GPR125_ENST00000282943.5_5'UTR	NM_145290.3	NP_660333.2	Q8IWK6	GP125_HUMAN	G protein-coupled receptor 125			56		Breast(46;0.198)			CTTCCACGCTCGTTGGGACAT	0.517000																								0							SO:0001819	synonymous_variant			ENST00000334304.5	1	0	hg19	CCDS33964.1																																																																																				TCGA-YB-A89D-01A-12D-A36O-08	GPR125-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362960.3	1	0	0	26	770	0	176	0	7.303879e-01	0	78	0	176	2		0	0	0	0	0	2	1	1.000000	26	749	0	176	2		0	0	0	0	176	2	-2.774725	1	1	0	0		1	2	2	4	2.119847	1	0.240000	3.280000	0.379896	0.340000	0.210000	1.000000	0.350000	0.375625	0.340000	0	2.700000e-01	4.300000e-01
RGS12	6002	broad.mit.edu	37	4	3419185	3419185	+	Missense_Mutation	SNP	G	G	T			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr4:3419185G>T	ENST00000344733.5	+	9	3582	c.2678G>T	c.(2677-2679)cGg>cTg	p.R893L	RGS12_ENST00000336727.3_Missense_Mutation_p.R893L|RGS12_ENST00000508158.1_3'UTR|RGS12_ENST00000306648.7_Missense_Mutation_p.R291L|RGS12_ENST00000538395.1_Missense_Mutation_p.R235L|RGS12_ENST00000338806.4_Missense_Mutation_p.R245L|RGS12_ENST00000382788.3_Missense_Mutation_p.R893L	NM_198229.2	NP_937872.1	O14924	RGS12_HUMAN	regulator of G-protein signaling 12			43					GAGAAGAAGCGGAAAGGCGCG	0.552000																								0							SO:0001583	missense			ENST00000344733.5	1	1	hg19	CCDS3366.1	.	.	.	.	.	.	.	.	.	.	G	14.12	2.440438	0.43326	.	.	ENSG00000159788	ENST00000344733;ENST00000336727;ENST00000382788;ENST00000306648;ENST00000338806;ENST00000538395	T;T;T;T;T;T	0.37235	1.49;1.49;1.49;1.21;1.23;1.26	4.34	4.34	0.51931	.	0.065361	0.64402	D	0.000019	T	0.49508	0.1561	M	0.65975	2.015	0.09310	N	0.999992	P;D;P;D;D;B;P;D;P	0.60575	0.896;0.988;0.802;0.988;0.977;0.393;0.896;0.968;0.937	P;P;P;P;D;B;P;P;P	0.63703	0.604;0.724;0.483;0.724;0.917;0.169;0.676;0.734;0.822	T	0.39418	-0.9615	10	0.42905	T	0.14	-19.7633	6.3948	0.21607	0.2155:0.0:0.7845:0.0	.	235;92;235;92;235;245;291;893;893	B7Z764;B3KVS7;B7Z8B8;A8K440;O14924-2;O14924-3;Q8WX95;O14924;O14924-4	.;.;.;.;.;.;.;RGS12_HUMAN;.	L	893;893;893;291;245;235	ENSP00000339381:R893L;ENSP00000338509:R893L;ENSP00000372238:R893L;ENSP00000304459:R291L;ENSP00000342133:R245L;ENSP00000438888:R235L	ENSP00000304459:R291L	R	+	2	0	RGS12	3388983	0.980000	0.34600	0.041000	0.18516	0.357000	0.29423	4.395000	0.59678	1.982000	0.57802	0.563000	0.77884	CGG		TCGA-YB-A89D-01A-12D-A36O-08	RGS12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206602.1	0	0	0	9	282	0	53	0	4.328002e-01	0	44	0	53	2		0	0	0	0	0	2	1	0.993554	9	274	0	52	2		0	0	0	0	53	2	-3.153069	1	1	0	0		1	2	2	4	2.119847	1	0.240000	3.280000	0.379896	0.330000	0.160000	1.000000	0.310000	0.377314	0.330000	0	2.300000e-01	4.800000e-01
ATP8A1	10396	broad.mit.edu	37	4	42581933	42581933	+	Missense_Mutation	SNP	C	C	A			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr4:42581933C>A	ENST00000381668.5	-	11	1128	c.897G>T	c.(895-897)ttG>ttT	p.L299F	ATP8A1_ENST00000264449.10_Missense_Mutation_p.L299F	NM_006095.2	NP_006086.1	Q9Y2Q0	AT8A1_HUMAN	ATPase, aminophospholipid transporter (APLT), class I, type 8A, member 1			51				Phosphatidylserine(DB00144)	AAAATAAAATCAAAATTTGTA	0.343000																								0							SO:0001583	missense			ENST00000381668.5	1	0	hg19	CCDS3466.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.570735	0.86542	.	.	ENSG00000124406	ENST00000381668;ENST00000264449	T;T	0.77750	-1.12;-1.12	5.66	5.66	0.87406	ATPase, P-type, ATPase-associated domain (1);	0.000000	0.64402	D	0.000001	D	0.88980	0.6585	M	0.78049	2.395	0.80722	D	1	D;D;D	0.89917	0.997;1.0;1.0	D;D;D	0.87578	0.995;0.998;0.997	D	0.89136	0.3513	10	0.72032	D	0.01	.	20.1225	0.97967	0.0:1.0:0.0:0.0	.	299;299;299	B4DII6;Q32M35;Q9Y2Q0	.;.;AT8A1_HUMAN	F	299	ENSP00000371084:L299F;ENSP00000264449:L299F	ENSP00000264449:L299F	L	-	3	2	ATP8A1	42276690	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	1.501000	0.35693	2.831000	0.97527	0.650000	0.86243	TTG		TCGA-YB-A89D-01A-12D-A36O-08	ATP8A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216861.2	1	0	0	11	209	0	37	0	1.722212e-02	0	4	0	37	2		0	0	0	0	0	2	1	0.998202	11	203	0	36	2		0	0	0	0	37	2	-4.665690	1	0	0	0		1	2	2	4	2.119847	1	0.240000	3.280000	0.379896	0.530000	0.280000	1.000000	0.510000	0.568776	0.530000	0	3.900000e-01	7.300000e-01
SPATA18	132671	broad.mit.edu	37	4	52960706	52960706	+	Missense_Mutation	SNP	G	G	A			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr4:52960706G>A	ENST00000295213.4	+	12	1951	c.1577G>A	c.(1576-1578)cGg>cAg	p.R526Q	SPATA18_ENST00000419395.2_Missense_Mutation_p.R494Q	NM_145263.2	NP_660306.1	Q8TC71	MIEAP_HUMAN	spermatogenesis associated 18			41			GBM - Glioblastoma multiforme(4;1.77e-13)|LUSC - Lung squamous cell carcinoma(32;0.00204)		TCTCGAAGTCGGAGTCCTTCT	0.348000																								0							SO:0001583	missense			ENST00000295213.4	1	1	hg19	CCDS3489.1	.	.	.	.	.	.	.	.	.	.	G	26.2	4.719010	0.89205	.	.	ENSG00000163071	ENST00000295213;ENST00000419395	T;T	0.36340	1.26;1.29	4.84	4.84	0.62591	.	0.197922	0.43579	D	0.000555	T	0.55955	0.1953	M	0.61703	1.905	0.38418	D	0.946104	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.995	T	0.60459	-0.7259	10	0.66056	D	0.02	-9.9646	13.6443	0.62272	0.0:0.0:1.0:0.0	.	494;526	Q8TC71-2;Q8TC71	.;MIEAP_HUMAN	Q	526;494	ENSP00000295213:R526Q;ENSP00000415309:R494Q	ENSP00000295213:R526Q	R	+	2	0	SPATA18	52655463	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	4.694000	0.61760	2.677000	0.91161	0.655000	0.94253	CGG		TCGA-YB-A89D-01A-12D-A36O-08	SPATA18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250597.2	1	0	1	118	478	0	99	1	3.413696e-01	3	3	0	99	2		0	0	0	0	0	2	1	1.000000	116	470	0	98	2		0	0	0	0	99	2	-2.732022	1	1	121412	1	33	1	2	2	4	2.119847	1	0.240000	3.280000	0.379896	0.990000	0.990000	1.000000	1.000000	1.000000	0.990000	1	9.900000e-01	1
DDX46	9879	broad.mit.edu	37	5	134109505	134109505	+	Silent	SNP	C	C	A	rs140064519		TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr5:134109505C>A	ENST00000354283.4	+	5	702	c.567C>A	c.(565-567)atC>atA	p.I189I	DDX46_ENST00000452510.2_Silent_p.I189I			Q7L014	DDX46_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 46			30			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)		AAAAGGAAATCGAAGAGATGA	0.353000													Colon(13;391 453 4901 21675 24897)											0							SO:0001819	synonymous_variant			ENST00000354283.4	1	0	hg19	CCDS34240.1																																																																																				TCGA-YB-A89D-01A-12D-A36O-08	DDX46-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371584.1	1	0	0	14	342	0	64	0	6.717840e-01	0	57	0	64	2		0	0	0	0	0	2	1	0.999733	13	336	0	64	2		0	0	0	0	64	2	-3.108651	1	1	0	0		1	1	2	3	1.962891	0	0.240000	3.280000	0.321429	0.370000	0.210000	0.590000	0.360000	0.388747	0.370000	0	2.800000e-01	4.800000e-01
PCDHA9	9752	broad.mit.edu	37	5	140228096	140228096	+	Nonsense_Mutation	SNP	C	C	T			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr5:140228096C>T	ENST00000532602.1	+	1	1049	c.16C>T	c.(16-18)Cga>Tga	p.R6*	PCDHA3_ENST00000522353.2_Intron|PCDHA9_ENST00000378122.3_Nonsense_Mutation_p.R6*|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA8_ENST00000531613.1_Intron	NM_031857.1	NP_114063.1	Q9Y5H5	PCDA9_HUMAN	protocadherin alpha 9			59			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		ATACTCAAGTCGAGGAGATCC	0.488000													Melanoma(55;1800 1972 14909)											0							SO:0001587	stop_gained			ENST00000532602.1	0	1	hg19	CCDS54920.1	.	.	.	.	.	.	.	.	.	.	C	39	7.294141	0.98192	.	.	ENSG00000204961	ENST00000532602;ENST00000378122	.	.	.	3.73	-0.921	0.10472	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.4352	0.16478	0.4129:0.2254:0.3617:0.0	.	.	.	.	X	6	.	ENSP00000367362:R6X	R	+	1	2	PCDHA9	140208280	0.000000	0.05858	0.000000	0.03702	0.187000	0.23431	-0.372000	0.07504	-0.010000	0.14271	0.591000	0.81541	CGA		TCGA-YB-A89D-01A-12D-A36O-08	PCDHA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372896.2	1	0	0	87	670	0	203		0	0	0	0	203	2		0	0	0	0	0	2	1	1.000000	85	663	0	201	2		0	0	0	0	203	2	-20.000000	1	0	0	0		1	1	2	3	1.962891	0	0.240000	3.280000	0.321429	0.990000	0.860000	1.000000	1.000000	0.985901	0.990000	1	9.600000e-01	1
ADAMTS2	9509	broad.mit.edu	37	5	178552049	178552049	+	Silent	SNP	G	G	A			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08			G	A	G	G		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr5:178552049G>A	ENST00000251582.7	-	19	2984	c.2883C>T	c.(2881-2883)gaC>gaT	p.D961D		NM_014244.4	NP_055059.2	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 2			72	all_cancers(89;0.000456)|all_epithelial(37;0.000138)|Renal(175;0.000159)|Lung NSC(126;0.00184)|all_lung(126;0.00326)	all_cancers(40;0.00604)|all_neural(177;0.00411)|Medulloblastoma(196;0.00508)|Lung NSC(249;0.0569)|all_lung(500;0.129)|all_hematologic(541;0.211)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		CGGGCCGGGCGTCATTGCAGT	0.701000																								0							SO:0001819	synonymous_variant			ENST00000251582.7	1	1	hg19	CCDS4444.1																																																																																				TCGA-YB-A89D-01A-12D-A36O-08	ADAMTS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253507.1	1	0	0	67	621	0	167	0	9.972718e-01	0	83	0	167	2		0	0	0	0	0	2	1	1.000000	65	597	0	162	2		0	0	0	0	167	2	-19.264120	1	1	121344	2	37	1	1	2	3	1.962891	0	0.240000	3.280000	0.321429	0.900000	0.710000	1.000000	1.000000	0.903044	0.900000	1	8.000000e-01	1
CCDC127	133957	broad.mit.edu	37	5	205888	205888	+	Nonsense_Mutation	SNP	G	G	A			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr5:205888G>A	ENST00000296824.3	-	3	439	c.307C>T	c.(307-309)Cga>Tga	p.R103*		NM_145265.2	NP_660308.1	Q96BQ5	CC127_HUMAN	coiled-coil domain containing 127			12			all cancers(22;0.0236)|Lung(60;0.113)		AGGGCTTCTCGGTAACTAGCA	0.498000																								0							SO:0001587	stop_gained			ENST00000296824.3	0	1	hg19	CCDS3852.1	.	.	.	.	.	.	.	.	.	.	G	14.75	2.629715	0.46944	.	.	ENSG00000164366	ENST00000296824	.	.	.	5.77	4.91	0.64330	.	0.120792	0.56097	D	0.000029	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.6082	14.1903	0.65635	0.0:0.0:0.8491:0.1509	.	.	.	.	X	103	.	ENSP00000296824:R103X	R	-	1	2	CCDC127	258888	1.000000	0.71417	0.944000	0.38274	0.475000	0.33008	2.365000	0.44196	1.457000	0.47850	-0.218000	0.12543	CGA		TCGA-YB-A89D-01A-12D-A36O-08	CCDC127-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365459.2	0	0	0	9	572	1	131	0	2.576326e-02	1	34	1	131	3		0	0	0	0	0	2	0	0.102451	9	561	1	129	16		0	0	0	1	131	2	-2.613582	1	1	0	0		1	1	2	3	1.951143	0	0.240000	3.280000	0.321429	0.140000	0.060000	0.260000	0.150000	0.159503	0.140000	0	1.000000e-01	2.100000e-01
IRX2	153572	broad.mit.edu	37	5	2749639	2749639	+	Missense_Mutation	SNP	C	C	T			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr5:2749639C>T	ENST00000382611.6	-	2	760	c.512G>A	c.(511-513)cGc>cAc	p.R171H	C5orf38_ENST00000505778.1_5'Flank|C5orf38_ENST00000334000.3_5'Flank|IRX2_ENST00000302057.5_Missense_Mutation_p.R171H|C5orf38_ENST00000457752.2_5'Flank|C5orf38_ENST00000397835.4_5'Flank|IRX2_ENST00000502957.1_5'UTR|C5orf38_ENST00000515640.1_5'Flank	NM_001134222.1	NP_001127694.1	Q9BZI1	IRX2_HUMAN	iroquois homeobox 2			26					CTTCTTGAGGCGCCGGCGCGC	0.592000																								0							SO:0001583	missense			ENST00000382611.6	0	1	hg19	CCDS3868.1	.	.	.	.	.	.	.	.	.	.	C	35	5.448586	0.96205	.	.	ENSG00000170561	ENST00000382611;ENST00000302057;ENST00000502957	D;D;D	0.98617	-5.03;-5.03;-5.03	4.85	4.85	0.62838	Homeodomain-related (1);Homeobox (2);Homeobox KN domain (1);Homeodomain-like (1);Homeobox, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.99471	0.9812	H	0.96996	3.92	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98132	1.0431	10	0.87932	D	0	-23.159	17.9697	0.89110	0.0:1.0:0.0:0.0	.	171	Q9BZI1	IRX2_HUMAN	H	171;171;78	ENSP00000372056:R171H;ENSP00000307006:R171H;ENSP00000426151:R78H	ENSP00000307006:R171H	R	-	2	0	IRX2	2802639	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.460000	0.80816	2.239000	0.73571	0.655000	0.94253	CGC		TCGA-YB-A89D-01A-12D-A36O-08	IRX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206749.2	0	0	0	9	497	0	123	0	5.600986e-02	0	19	0	123	2		0	0	0	0	0	2	1	0.993754	9	487	0	119	2		0	0	0	0	123	2	-2.146419	0	1	0	0		1	1	2	3	1.951143	0	0.240000	3.280000	0.321429	0.170000	0.070000	0.300000	0.160000	0.182955	0.170000	0	1.200000e-01	2.400000e-01
NNT	23530	broad.mit.edu	37	5	43624206	43624206	+	Silent	SNP	C	C	A			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr5:43624206C>A	ENST00000264663.5	+	6	981	c.760C>A	c.(760-762)Cga>Aga	p.R254R	NNT_ENST00000512996.2_Silent_p.R123R|NNT_ENST00000344920.4_Silent_p.R254R	NM_012343.3	NP_036475.3	Q13423	NNTM_HUMAN	nicotinamide nucleotide transhydrogenase	p.R254R(1)		51	Lung NSC(6;2.58e-06)				TGCAATTGTTCGAGGATTTGA	0.413000																								1	Substitution - coding silent(1)						SO:0001819	synonymous_variant			ENST00000264663.5	1	0	hg19	CCDS3949.1																																																																																				TCGA-YB-A89D-01A-12D-A36O-08	NNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214026.1	1	0	0	44	968	0	221	0	4.443647e-01	0	34	0	221	2		0	0	0	0	0	2	1	1.000000	46	954	0	215	2		0	0	0	0	221	2	-4.136119	1	0	0	0		1	1	2	3	1.951143	0	0.240000	3.280000	0.321429	0.400000	0.290000	0.530000	0.400000	0.413336	0.400000	0	3.400000e-01	4.700000e-01
MCCC2	64087	broad.mit.edu	37	5	70931068	70931068	+	Silent	SNP	C	C	A			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr5:70931068C>A	ENST00000340941.6	+	10	1123	c.994C>A	c.(994-996)Cga>Aga	p.R332R	MCCC2_ENST00000509358.2_Silent_p.R332R|MCCC2_ENST00000510895.2_3'UTR|MCCC2_ENST00000323375.8_Silent_p.R294R	NM_022132.4	NP_071415.1	Q9HCC0	MCCB_HUMAN	methylcrotonoyl-CoA carboxylase 2 (beta)			30		Lung NSC(167;0.000697)|Prostate(74;0.0107)|Ovarian(174;0.0175)|Breast(144;0.198)		Biotin(DB00121)	CTTTGATGTCCGAGAGGTATG	0.393000																								0		GRCh37	CM053319	MCCC2	M		SO:0001819	synonymous_variant			ENST00000340941.6	0	1	hg19	CCDS34184.1																																																																																				TCGA-YB-A89D-01A-12D-A36O-08	MCCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369243.4	0	0	0	7	398	0	103	0	2.297523e-01	0	46	0	103	2		0	0	0	0	0	2	1	0.980118	7	394	0	102	2		0	0	0	0	103	2	-2.666817	1	1	0	0		1	0	2	2	1.746669	1	0.240000	3.280000	0.240000	0.150000	0.060000	0.280000	0.140000	0.162506	0.150000	0	1.000000e-01	2.200000e-01
GFM2	84340	broad.mit.edu	37	5	74026094	74026094	+	Missense_Mutation	SNP	G	G	T			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr5:74026094G>T	ENST00000296805.3	-	17	2174	c.1717C>A	c.(1717-1719)Cgt>Agt	p.R573S	GFM2_ENST00000345239.2_Missense_Mutation_p.R526S|GFM2_ENST00000515125.1_Intron|GFM2_ENST00000509430.1_Missense_Mutation_p.R573S	NM_032380.3	NP_115756.2			G elongation factor, mitochondrial 2			14		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Breast(144;0.231)			CCTGTGGCACGAACTGAGTTT	0.398000																								0							SO:0001583	missense			ENST00000296805.3	1	0	hg19	CCDS4023.1	.	.	.	.	.	.	.	.	.	.	G	6.416	0.444897	0.12164	.	.	ENSG00000164347	ENST00000296805;ENST00000345239;ENST00000509430	T;T;T	0.28895	1.59;1.59;1.59	5.64	2.93	0.34026	Ribosomal protein S5 domain 2-type fold (1);Translation elongation factor EFG/EF2, domain IV (2);Ribosomal protein S5 domain 2-type fold, subgroup (1);	0.474700	0.25186	N	0.032482	T	0.18964	0.0455	L	0.28556	0.865	0.09310	N	1	B;B;B	0.11235	0.002;0.004;0.003	B;B;B	0.15484	0.008;0.006;0.013	T	0.17623	-1.0363	10	0.35671	T	0.21	-0.3872	5.1057	0.14783	0.2806:0.0:0.5859:0.1335	.	573;526;573	Q969S9-3;Q969S9-2;Q969S9	.;.;RRF2M_HUMAN	S	573;526;573	ENSP00000296805:R573S;ENSP00000296804:R526S;ENSP00000427004:R573S	ENSP00000296805:R573S	R	-	1	0	GFM2	74061850	0.338000	0.24775	0.818000	0.32626	0.977000	0.68977	1.075000	0.30716	0.341000	0.23771	-0.263000	0.10527	CGT		TCGA-YB-A89D-01A-12D-A36O-08	GFM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219860.2	1	0	0	10	283	0	56	0	1.998702e-01	0	22	0	56	2		0	0	0	0	0	2	1	0.996626	9	277	0	56	2		0	0	0	0	56	2	-3.057998	1	1	0	0		1	0	2	2	1.746669	1	0.240000	3.280000	0.240000	0.290000	0.140000	0.490000	0.280000	0.307374	0.290000	0	2.100000e-01	3.900000e-01
COL4A3BP	10087	broad.mit.edu	37	5	74754979	74754979	+	Missense_Mutation	SNP	C	C	A			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr5:74754979C>A	ENST00000405807.4	-	3	680	c.259G>T	c.(259-261)Gat>Tat	p.D87Y	COL4A3BP_ENST00000380494.5_Missense_Mutation_p.D215Y|COL4A3BP_ENST00000261415.7_Missense_Mutation_p.D87Y	NM_005713.2	NP_005704.1	Q9Y5P4	C43BP_HUMAN	collagen, type IV, alpha 3 (Goodpasture antigen) binding protein			16		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Prostate(461;0.174)			ACACTAATATCAAATCGACAT	0.378000																								0							SO:0001583	missense			ENST00000405807.4	0	1	hg19	CCDS4028.1	.	.	.	.	.	.	.	.	.	.	C	26.5	4.742024	0.89573	.	.	ENSG00000113163	ENST00000405807;ENST00000380494;ENST00000261415	T;T;T	0.12465	2.68;2.68;2.68	5.35	5.35	0.76521	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.85682	D	0.000000	T	0.37598	0.1009	M	0.62088	1.915	0.80722	D	1	D;D;D	0.76494	0.999;0.998;0.999	D;D;D	0.87578	0.998;0.996;0.998	T	0.09422	-1.0675	10	0.87932	D	0	-1.6075	18.6597	0.91468	0.0:1.0:0.0:0.0	.	87;215;87	Q9Y5P4;Q9Y5P4-3;Q9Y5P4-2	C43BP_HUMAN;.;.	Y	87;215;87	ENSP00000383996:D87Y;ENSP00000369862:D215Y;ENSP00000261415:D87Y	ENSP00000261415:D87Y	D	-	1	0	COL4A3BP	74790735	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.682000	0.84083	2.493000	0.84123	0.563000	0.77884	GAT		TCGA-YB-A89D-01A-12D-A36O-08	COL4A3BP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219875.2	0	0	0	8	353	0	94	0	9.880206e-02	0	21	0	94	2		0	0	0	0	0	2	1	0.988820	8	347	0	94	2		0	0	0	0	94	2	-8.151397	1	1	0	0		1	0	2	2	1.746669	1	0.240000	3.280000	0.240000	0.190000	0.080000	0.340000	0.180000	0.204788	0.190000	0	1.300000e-01	2.700000e-01
RTN4IP1	84816	broad.mit.edu	37	6	107070789	107070789	+	Silent	SNP	G	G	T			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr6:107070789G>T	ENST00000369063.3	-	2	795	c.330C>A	c.(328-330)atC>atA	p.I110I	RTN4IP1_ENST00000539449.1_Silent_p.I110I	NM_032730.4	NP_116119.2	Q8WWV3	RT4I1_HUMAN	reticulon 4 interacting protein 1			13	Breast(9;0.0107)|all_epithelial(6;0.14)	all_cancers(87;9.45e-05)|Acute lymphoblastic leukemia(125;2.13e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.0144)	Epithelial(6;0.000873)|all cancers(7;0.00363)|BRCA - Breast invasive adenocarcinoma(8;0.00721)|OV - Ovarian serous cystadenocarcinoma(5;0.0394)		CTTCTCCTTTGATTTTCACGT	0.413000																								0							SO:0001819	synonymous_variant			ENST00000369063.3	1	0	hg19	CCDS5056.1																																																																																				TCGA-YB-A89D-01A-12D-A36O-08	RTN4IP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041673.1	1	0	0	17	434	0	118	0	3.014482e-02	0	7	0	118	2		0	0	0	0	0	2	1	0.999962	17	427	0	117	2		0	0	0	0	118	2	-4.077091	1	1	0	0		1	0	2	2	1.747676	1	0.240000	3.280000	0.240000	0.310000	0.190000	0.480000	0.310000	0.328793	0.310000	0	2.400000e-01	4.000000e-01
PTPRK	5796	broad.mit.edu	37	6	128404925	128404925	+	Nonsense_Mutation	SNP	C	C	A			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr6:128404925C>A	ENST00000368215.3	-	9	1509	c.1510G>T	c.(1510-1512)Gaa>Taa	p.E504*	PTPRK_ENST00000368227.3_Nonsense_Mutation_p.E504*|PTPRK_ENST00000368226.4_Nonsense_Mutation_p.E504*|RP11-103C16.2_ENST00000417390.1_RNA|PTPRK_ENST00000532331.1_Nonsense_Mutation_p.E504*|PTPRK_ENST00000368213.5_Nonsense_Mutation_p.E504*|PTPRK_ENST00000368207.3_Nonsense_Mutation_p.E504*|PTPRK_ENST00000524481.1_5'UTR|PTPRK_ENST00000368210.3_Nonsense_Mutation_p.E504*			Q15262	PTPRK_HUMAN	protein tyrosine phosphatase, receptor type, K		PTPRK/RSPO3(10)	72					ATCTTATTTTCAAAGGATGTT	0.348000																								0							SO:0001587	stop_gained			ENST00000368215.3	0	1	hg19		.	.	.	.	.	.	.	.	.	.	C	39	7.548767	0.98352	.	.	ENSG00000152894	ENST00000368226;ENST00000368227;ENST00000532331;ENST00000368213;ENST00000368210;ENST00000368215;ENST00000368207;ENST00000427676	.	.	.	6.02	5.15	0.70609	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.30078	T	0.28	.	16.7022	0.85357	0.1306:0.8694:0.0:0.0	.	.	.	.	X	504;504;504;504;504;504;504;361	.	ENSP00000357190:E504X	E	-	1	0	PTPRK	128446618	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.625000	0.83145	1.527000	0.49086	-0.188000	0.12872	GAA		TCGA-YB-A89D-01A-12D-A36O-08	PTPRK-005	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000042163.1	0	0	0	7	423	0	74	0	1.351923e-01	0	34	0	74	2		0	0	0	0	0	2	1	0.979970	7	418	0	70	2		0	0	0	0	74	2	-2.762026	1	1	0	0		1	0	2	2	1.747676	1	0.240000	3.280000	0.240000	0.140000	0.050000	0.260000	0.140000	0.153170	0.140000	0	9.000000e-02	2.000000e-01
FUCA2	2519	broad.mit.edu	37	6	143823168	143823168	+	Missense_Mutation	SNP	C	C	A			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr6:143823168C>A	ENST00000002165.6	-	5	1110	c.1055G>T	c.(1054-1056)cGa>cTa	p.R352L	RP1-20N2.6_ENST00000591189.1_RNA|RP1-20N2.6_ENST00000593045.1_RNA|RP1-20N2.6_ENST00000591892.1_RNA|RP1-20N2.6_ENST00000589563.1_RNA|RP1-20N2.6_ENST00000610068.1_RNA|RP1-20N2.6_ENST00000589489.1_RNA|RP1-20N2.6_ENST00000590703.1_RNA|RP1-20N2.6_ENST00000415586.1_RNA|RP1-20N2.6_ENST00000593175.1_RNA|FUCA2_ENST00000367585.1_5'UTR|FUCA2_ENST00000438118.2_3'UTR	NM_032020.4	NP_114409.2	Q9BTY2	FUCO2_HUMAN	fucosidase, alpha-L- 2, plasma			9					TTGCCTCAGTCGCTCCTCAAA	0.443000																								0							SO:0001583	missense			ENST00000002165.6	0	1	hg19	CCDS5200.1	.	.	.	.	.	.	.	.	.	.	C	35	5.462906	0.96257	.	.	ENSG00000001036	ENST00000002165;ENST00000451668	T;T	0.58358	0.34;0.34	5.98	5.98	0.97165	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.000000	0.85682	D	0.000000	T	0.72211	0.3432	M	0.84511	2.7	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.67898	-0.5551	10	0.30854	T	0.27	-21.6749	20.4581	0.99154	0.0:1.0:0.0:0.0	.	31;352	Q7Z6V2;Q9BTY2	.;FUCO2_HUMAN	L	352;31	ENSP00000002165:R352L;ENSP00000398119:R31L	ENSP00000002165:R352L	R	-	2	0	FUCA2	143864861	1.000000	0.71417	0.910000	0.35882	0.949000	0.60115	7.445000	0.80570	2.835000	0.97688	0.650000	0.86243	CGA		TCGA-YB-A89D-01A-12D-A36O-08	FUCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042521.2	0	0	0	9	451	0	102	0	9.273512e-01	0	233	0	102	2		0	0	0	0	0	2	1	0.994141	9	448	0	100	2		0	0	0	0	102	2	-3.043248	1	1	0	0		1	0	2	2	1.747676	1	0.240000	3.280000	0.240000	0.160000	0.070000	0.290000	0.160000	0.179120	0.160000	0	1.100000e-01	2.300000e-01
PLEKHG1	57480	broad.mit.edu	37	6	151153189	151153189	+	Missense_Mutation	SNP	G	G	A	rs113595784		TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr6:151153189G>A	ENST00000358517.2	+	15	3153	c.2942G>A	c.(2941-2943)cGg>cAg	p.R981Q	PLEKHG1_ENST00000367328.1_Missense_Mutation_p.R981Q			Q9ULL1	PKHG1_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 1			53			BRCA - Breast invasive adenocarcinoma(37;0.0923)		ATGATGGCTCGGCAGTACAGT	0.507000																								0							SO:0001583	missense			ENST00000358517.2	0	1	hg19	CCDS34552.1	.	.	.	.	.	.	.	.	.	.	G	35	5.451520	0.96205	.	.	ENSG00000120278	ENST00000367328;ENST00000358517	T;T	0.30448	1.53;1.53	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	T	0.50888	0.1642	M	0.68952	2.095	0.52501	D	0.999954	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.998;0.998	T	0.51108	-0.8747	10	0.87932	D	0	.	20.0825	0.97783	0.0:0.0:1.0:0.0	.	788;981;981	Q5EBL9;Q5JYA6;Q9ULL1	.;.;PKHG1_HUMAN	Q	981	ENSP00000356297:R981Q;ENSP00000351318:R981Q	ENSP00000351318:R981Q	R	+	2	0	PLEKHG1	151194882	1.000000	0.71417	0.996000	0.52242	0.983000	0.72400	9.476000	0.97823	2.746000	0.94184	0.655000	0.94253	CGG		TCGA-YB-A89D-01A-12D-A36O-08	PLEKHG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042691.1	0	0	0	12	777	0	214	0	2.253937e-02	1	13	0	214	2		0	0	0	0	0	2	1	0.999030	12	765	0	211	2		0	0	0	0	214	2	-1.968841	0	1	121412	5	42	1	0	2	2	1.747676	1	0.240000	3.280000	0.240000	0.120000	0.060000	0.210000	0.120000	0.136391	0.120000	0	9.000000e-02	1.700000e-01
TCP1	6950	broad.mit.edu	37	6	160202137	160202137	+	Missense_Mutation	SNP	G	G	A			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr6:160202137G>A	ENST00000321394.7	-	8	1083	c.803C>T	c.(802-804)tCa>tTa	p.S268L	SNORA20_ENST00000384662.1_RNA|TCP1_ENST00000420894.2_Missense_Mutation_p.S268L|TCP1_ENST00000544255.1_Missense_Mutation_p.S44L|TCP1_ENST00000392168.2_Missense_Mutation_p.S113L	NM_030752.2	NP_110379.2	P17987	TCPA_HUMAN	t-complex 1			10		Breast(66;1.53e-05)|Ovarian(120;0.024)			GGTGATATCTGATTCTCTGCA	0.328000																								0							SO:0001583	missense			ENST00000321394.7	1	1	hg19	CCDS5269.1	.	.	.	.	.	.	.	.	.	.	G	13.53	2.264755	0.40095	.	.	ENSG00000120438	ENST00000321394;ENST00000544255;ENST00000420894;ENST00000392168;ENST00000539756	T;T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19;-1.19	5.63	5.63	0.86233	.	0.054590	0.85682	D	0.000000	T	0.43722	0.1260	N	0.04508	-0.205	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.14578	0.002;0.011	T	0.50381	-0.8835	10	0.10902	T	0.67	-8.3473	19.6959	0.96026	0.0:0.0:1.0:0.0	.	268;268	E7ERF2;P17987	.;TCPA_HUMAN	L	268;44;268;113;66	ENSP00000317334:S268L;ENSP00000439447:S44L;ENSP00000390159:S268L;ENSP00000376008:S113L;ENSP00000441345:S66L	ENSP00000317334:S268L	S	-	2	0	TCP1	160122127	1.000000	0.71417	0.978000	0.43139	0.911000	0.54048	7.367000	0.79558	2.659000	0.90383	0.650000	0.86243	TCA		TCGA-YB-A89D-01A-12D-A36O-08	TCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042917.2	1	0	1	67	520	0	121	1	1	39	313	0	121	2		0	0	0	0	0	2	1	1.000000	68	516	0	121	2		0	0	0	0	121	2	-19.999780	1	0	0	0		1	0	2	2	1.747676	1	0.240000	3.280000	0.240000	0.940000	0.740000	1.000000	1.000000	0.931043	0.940000	1	8.400000e-01	1
ZNF311	282890	broad.mit.edu	37	6	28963821	28963821	+	Silent	SNP	G	G	T			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr6:28963821G>T	ENST00000377179.3	-	7	1470	c.958C>A	c.(958-960)Cga>Aga	p.R320R	ZNF311_ENST00000483450.1_5'UTR	NM_001010877.2	NP_001010877.2	Q5JNZ3	ZN311_HUMAN	zinc finger protein 311			28					TTTTTATGTCGGCAAAGAGCT	0.493000																								0							SO:0001819	synonymous_variant			ENST00000377179.3	0	1	hg19	CCDS34357.1																																																																																				TCGA-YB-A89D-01A-12D-A36O-08	ZNF311-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076631.3	0	0	0	11	415	0	94	0	0	0	1	0	94	2		0	0	0	0	0	2	1	0.998223	11	408	0	94	2		0	0	0	0	94	2	-2.937220	1	1	0	0		1	0	2	2	1.774194	1	0.240000	3.280000	0.240000	0.220000	0.110000	0.370000	0.220000	0.231897	0.220000	0	1.600000e-01	2.900000e-01
DLK2	65989	broad.mit.edu	37	6	43418947	43418947	+	Missense_Mutation	SNP	C	C	T			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr6:43418947C>T	ENST00000357338.3	-	6	1182	c.482G>A	c.(481-483)cGc>cAc	p.R161H	DLK2_ENST00000372488.3_Missense_Mutation_p.R161H|DLK2_ENST00000372485.1_Missense_Mutation_p.R155H|DLK2_ENST00000414245.1_Missense_Mutation_p.R155H	NM_206539.1	NP_996262.1	Q6UY11	DLK2_HUMAN	delta-like 2 homolog (Drosophila)			7	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0152)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)		CACCAAGCAGCGGCACGTGAA	0.592000																								0							SO:0001583	missense			ENST00000357338.3	1	1	hg19	CCDS4897.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.07|18.07	3.542004|3.542004	0.65198|0.65198	.|.	.|.	ENSG00000171462|ENSG00000171462	ENST00000430324|ENST00000372485;ENST00000372488;ENST00000357338;ENST00000414245	.|D;D;D;D	.|0.87809	.|-2.3;-2.3;-2.3;-2.3	4.51|4.51	4.51|4.51	0.55191|0.55191	.|Epidermal growth factor-like (1);EGF-like region, conserved site (2);Epidermal growth factor-like, type 3 (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.67297|0.67297	0.2878|0.2878	N|N	0.21373|0.21373	0.66|0.66	0.46167|0.46167	D|D	0.998909|0.998909	.|P	.|0.51240	.|0.943	.|B	.|0.40410	.|0.328	T|T	0.68655|0.68655	-0.5351|-0.5351	5|10	.|0.19147	.|T	.|0.46	.|.	12.2573|12.2573	0.54631|0.54631	0.0:0.9171:0.0:0.0829|0.0:0.9171:0.0:0.0829	.|.	.|161	.|Q6UY11	.|DLK2_HUMAN	T|H	67|155;161;161;155	.|ENSP00000361563:R155H;ENSP00000361566:R161H;ENSP00000349893:R161H;ENSP00000398906:R155H	.|ENSP00000349893:R161H	A|R	-|-	1|2	0|0	DLK2|DLK2	43526925|43526925	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.838000|0.838000	0.47535|0.47535	2.486000|2.486000	0.45259|0.45259	2.507000|2.507000	0.84556|0.84556	0.455000|0.455000	0.32223|0.32223	GCT|CGC		TCGA-YB-A89D-01A-12D-A36O-08	DLK2-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040618.1	0	0	0	6	170	0	36	0	1.757580e-03	0	2	0	36	2		0	0	0	0	0	2	1	0.963897	6	167	0	36	2		0	0	0	0	36	2	-8.137891	1	1	121412	3	32	1	0	2	2	1.747676	1	0.240000	3.280000	0.240000	0.300000	0.120000	0.570000	0.280000	0.321837	0.300000	0	1.900000e-01	4.300000e-01
MEP1A	4224	broad.mit.edu	37	6	46797278	46797278	+	Missense_Mutation	SNP	C	C	A			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr6:46797278C>A	ENST00000230588.4	+	10	1123	c.1114C>A	c.(1114-1116)Cgc>Agc	p.R372S		NM_005588.2	NP_005579.2	Q16819	MEP1A_HUMAN	meprin A, alpha (PABA peptide hydrolase)			42			Lung(136;0.192)		AGGCAATGTTCGCAAGTTGGT	0.488000																								0							SO:0001583	missense			ENST00000230588.4	0	1	hg19	CCDS4918.1	.	.	.	.	.	.	.	.	.	.	C	13.75	2.330826	0.41297	.	.	ENSG00000112818	ENST00000230588	T	0.02067	4.47	5.77	4.89	0.63831	Concanavalin A-like lectin/glucanase (1);MAM domain (3);	0.342421	0.34435	N	0.003979	T	0.03783	0.0107	M	0.74881	2.28	0.43522	D	0.995798	D;D	0.58970	0.984;0.984	P;P	0.61070	0.858;0.883	T	0.53753	-0.8394	10	0.19147	T	0.46	-12.7042	10.0322	0.42107	0.1364:0.7941:0.0:0.0695	.	400;372	B7ZL91;Q16819	.;MEP1A_HUMAN	S	372	ENSP00000230588:R372S	ENSP00000230588:R372S	R	+	1	0	MEP1A	46905237	0.011000	0.17503	0.879000	0.34478	0.799000	0.45148	0.779000	0.26746	1.410000	0.46936	0.650000	0.86243	CGC		TCGA-YB-A89D-01A-12D-A36O-08	MEP1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040803.1	0	0	0	14	640	0	175	0	1.631920e-03	0	3	0	175	2		0	0	0	0	0	2	1	0.999742	15	635	0	174	2		0	0	0	0	175	2	-2.218927	0	1	0	0		1	0	2	2	1.747676	1	0.240000	3.280000	0.240000	0.180000	0.090000	0.290000	0.180000	0.189611	0.180000	0	1.300000e-01	2.400000e-01
LY86	9450	broad.mit.edu	37	6	6625213	6625213	+	Nonsense_Mutation	SNP	C	C	A			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr6:6625213C>A	ENST00000379953.2	+	3	543	c.191C>A	c.(190-192)tCa>tAa	p.S64*	LY86-AS1_ENST00000429345.1_RNA|LY86-AS1_ENST00000606044.1_RNA|LY86-AS1_ENST00000607278.1_RNA|LY86_ENST00000230568.4_Nonsense_Mutation_p.S64*|LY86-AS1_ENST00000435641.1_RNA			O95711	LY86_HUMAN	lymphocyte antigen 86			8	Ovarian(93;0.0377)				CAATTAAAATCAAATATCAAC	0.313000																								0							SO:0001587	stop_gained			ENST00000379953.2	0	1	hg19	CCDS4498.1	.	.	.	.	.	.	.	.	.	.	C	17.61	3.432933	0.62844	.	.	ENSG00000112799	ENST00000379953;ENST00000230568	.	.	.	5.26	3.22	0.36961	.	1.944890	0.02311	N	0.072065	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05620	T	0.96	4.3632	12.8308	0.57744	0.3071:0.6929:0.0:0.0	.	.	.	.	X	64	.	ENSP00000230568:S64X	S	+	2	0	LY86	6570212	0.001000	0.12720	0.017000	0.16124	0.635000	0.38103	0.857000	0.27831	1.177000	0.42855	0.655000	0.94253	TCA		TCGA-YB-A89D-01A-12D-A36O-08	LY86-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039762.2	0	0	0	8	195	0	44	0	7.259222e-01	0	63	0	44	2		0	0	0	0	0	2	1	0.989153	8	192	0	44	2		0	0	0	0	44	2	-10.383520	1	1	0	0		1	0	2	2	1.735377	1	0.240000	3.280000	0.240000	0.340000	0.160000	0.600000	0.320000	0.360160	0.340000	0	2.300000e-01	4.700000e-01
COX7A2	1347	broad.mit.edu	37	6	75950955	75950955	+	Silent	SNP	C	C	A	rs139079443		TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr6:75950955C>A	ENST00000230459.4	-	2	238	c.45G>T	c.(43-45)acG>acT	p.T15T	COX7A2_ENST00000370081.2_Silent_p.T47T|COX7A2_ENST00000509698.1_Silent_p.T15T|COX7A2_ENST00000460985.1_Intron|COX7A2_ENST00000370089.2_Silent_p.T47T|COX7A2_ENST00000472311.2_Silent_p.T15T	NM_001865.3	NP_001856.2	P14406	CX7A2_HUMAN	cytochrome c oxidase subunit VIIa polypeptide 2 (liver)	p.T15T(1)		3					CAGTGCTTATCGTCCTCTGCC	0.358000																								1	Substitution - coding silent(1)						SO:0001819	synonymous_variant			ENST00000230459.4	0	1	hg19																																																																																					TCGA-YB-A89D-01A-12D-A36O-08	COX7A2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		0	0	0	11	848	0	177	0	9.845201e-01	0	543	0	177	2		0	0	0	0	0	2	1	0.998200	11	837	0	176	2		0	0	0	0	177	2	-2.341395	0	1	0	0		1	0	2	2	1.747676	1	0.240000	3.280000	0.240000	0.100000	0.050000	0.180000	0.100000	0.115699	0.100000	0	7.000000e-02	1.500000e-01
SENP6	26054	broad.mit.edu	37	6	76425185	76425185	+	Silent	SNP	C	C	A			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr6:76425185C>A	ENST00000447266.2	+	24	3692	c.3214C>A	c.(3214-3216)Cga>Aga	p.R1072R	SENP6_ENST00000370014.3_Silent_p.R1072R|SENP6_ENST00000370010.2_Silent_p.R1065R|SENP6_ENST00000541192.1_3'UTR	NM_015571.2	NP_056386.2	Q9GZR1	SENP6_HUMAN	SUMO1/sentrin specific peptidase 6			27		all_hematologic(105;0.189)			AGAAGAAATCCGAAACATAAT	0.368000																								0							SO:0001819	synonymous_variant			ENST00000447266.2	0	1	hg19	CCDS47454.1																																																																																				TCGA-YB-A89D-01A-12D-A36O-08	SENP6-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041272.2	0	0	0	8	519	0	144	0	5.412422e-01	0	111	0	144	2		0	0	0	0	0	2	1	0.988786	8	511	0	142	2		0	0	0	0	144	2	-2.237860	0	1	120806	1	35	1	0	2	2	1.747676	1	0.240000	3.280000	0.240000	0.130000	0.050000	0.240000	0.120000	0.140909	0.130000	0	8.000000e-02	1.900000e-01
FLNC	2318	broad.mit.edu	37	7	128491395	128491395	+	Silent	SNP	C	C	G			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr7:128491395C>G	ENST00000325888.8	+	34	5910	c.5649C>G	c.(5647-5649)gtC>gtG	p.V1883V	RP11-309L24.2_ENST00000469965.1_RNA|FLNC_ENST00000346177.6_Silent_p.V1850V	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma			128					TCACTATTGTCACCAAAGATG	0.587000																								0							SO:0001819	synonymous_variant			ENST00000325888.8	0	1	hg19	CCDS43644.1																																																																																				TCGA-YB-A89D-01A-12D-A36O-08	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059948.3	0	0	0	5	292	0	56	0	4.305680e-02	0	16	0	56	2		0	0	0	0	0	2	1	0.936397	5	289	0	56	2		0	0	0	0	56	2	-5.797591	1	0	0	0		1	2	2	4	2.158329	1	0.240000	3.280000	0.387097	0.180000	0.060000	0.380000	0.160000	0.206265	0.180000	0	1.100000e-01	2.900000e-01
ASB10	136371	broad.mit.edu	37	7	150878170	150878170	+	Silent	SNP	G	G	T			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr7:150878170G>T	ENST00000420175.2	-	3	984	c.960C>A	c.(958-960)gcC>gcA	p.A320A	ASB10_ENST00000434669.1_Silent_p.A365A|ASB10_ENST00000422024.1_Silent_p.A365A|ASB10_ENST00000275838.1_Silent_p.A320A|ASB10_ENST00000377867.3_Silent_p.A305A			Q8WXI3	ASB10_HUMAN	ankyrin repeat and SOCS box containing 10			12			OV - Ovarian serous cystadenocarcinoma(82;0.00448)		CCATGGTGTTGGCGCTGACAC	0.682000																								0							SO:0001819	synonymous_variant			ENST00000420175.2	0	1	hg19	CCDS47750.2																																																																																				TCGA-YB-A89D-01A-12D-A36O-08	ASB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347096.3	0	0	0	6	274	0	55		0	0	0	0	55	2		0	0	0	0	0	2	1	0.964256	4	274	0	55	2		0	0	0	0	55	2	-6.979241	1	0	0	0		1	2	2	4	2.166993	1	0.240000	3.280000	0.387097	0.230000	0.090000	0.450000	0.230000	0.255063	0.230000	0	1.500000e-01	3.400000e-01
KLHL7	55975	broad.mit.edu	37	7	23183515	23183515	+	Missense_Mutation	SNP	C	C	A			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr7:23183515C>A	ENST00000339077.5	+	6	907	c.664C>A	c.(664-666)Cgc>Agc	p.R222S	KLHL7_ENST00000322231.7_Missense_Mutation_p.R200S|KLHL7_ENST00000545443.1_Missense_Mutation_p.R200S|KLHL7_ENST00000539124.1_Missense_Mutation_p.R146S|KLHL7_ENST00000409689.1_Missense_Mutation_p.R174S|KLHL7_ENST00000479288.1_3'UTR|KLHL7_ENST00000542558.1_5'UTR	NM_001031710.2	NP_001026880.2	Q8IXQ5	KLHL7_HUMAN	kelch-like family member 7			25					TGAACCTAATCGCCAGCCATT	0.378000																								0							SO:0001583	missense			ENST00000339077.5	0	1	hg19	CCDS34609.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.603408	0.87157	.	.	ENSG00000122550	ENST00000536369;ENST00000322231;ENST00000339077;ENST00000539124;ENST00000409689;ENST00000545443	T;T;T;T;T	0.73258	-0.73;-0.73;-0.73;-0.73;-0.73	5.43	5.43	0.79202	BTB/Kelch-associated (2);	0.000000	0.85682	D	0.000000	D	0.87815	0.6272	M	0.91354	3.2	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.71870	0.975;0.957	D	0.90023	0.4129	10	0.87932	D	0	.	19.5857	0.95489	0.0:1.0:0.0:0.0	.	222;200	Q8IXQ5;Q8IXQ5-2	KLHL7_HUMAN;.	S	188;200;222;146;174;200	ENSP00000322958:R200S;ENSP00000343273:R222S;ENSP00000441136:R146S;ENSP00000386263:R174S;ENSP00000442366:R200S	ENSP00000322958:R200S	R	+	1	0	KLHL7	23150040	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.276000	0.58933	2.696000	0.92011	0.591000	0.81541	CGC		TCGA-YB-A89D-01A-12D-A36O-08	KLHL7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326860.3	0	0	0	13	1108	0	251	0	4.611809e-02	0	27	0	251	2		0	0	0	0	0	2	1	0.999460	12	1088	0	250	2		0	0	0	0	251	2	-2.287399	0	1	0	0		1	2	2	4	2.139765	1	0.240000	3.280000	0.385908	0.120000	0.050000	0.210000	0.120000	0.128318	0.120000	0	8.000000e-02	1.700000e-01
UBE2D4	51619	broad.mit.edu	37	7	43990227	43990227	+	Missense_Mutation	SNP	G	G	T			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr7:43990227G>T	ENST00000222402.3	+	6	423	c.334G>T	c.(334-336)Gac>Tac	p.D112Y	RP5-1165K10.2_ENST00000454572.1_RNA|POLR2J4_ENST00000427076.1_RNA|UBE2D4_ENST00000394798.4_Missense_Mutation_p.D74Y	NM_015983.3	NP_057067.1	Q9Y2X8	UB2D4_HUMAN	ubiquitin-conjugating enzyme E2D 4 (putative)			5					GCTGCTCTGCGACCCCAACCC	0.562000													Esophageal Squamous(27;401 815 16344 30604)											0							SO:0001583	missense			ENST00000222402.3	1	0	hg19	CCDS5474.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.025689	0.75390	.	.	ENSG00000078967	ENST00000222402;ENST00000394798	T;T	0.73789	-0.78;-0.78	4.49	3.61	0.41365	Ubiquitin-conjugating enzyme, E2 (2);Ubiquitin-conjugating enzyme/RWD-like (2);	0.055533	0.64402	D	0.000002	D	0.86834	0.6028	M	0.90369	3.11	0.58432	D	0.999999	D;D	0.89917	0.999;1.0	D;D	0.77557	0.976;0.99	D	0.87620	0.2509	10	0.87932	D	0	.	10.2569	0.43403	0.0996:0.0:0.9004:0.0	.	74;112	Q9UQL0;Q9Y2X8	.;UB2D4_HUMAN	Y	112;74	ENSP00000222402:D112Y;ENSP00000378277:D74Y	ENSP00000222402:D112Y	D	+	1	0	UBE2D4	43956752	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	8.286000	0.89916	0.885000	0.36088	0.655000	0.94253	GAC		TCGA-YB-A89D-01A-12D-A36O-08	UBE2D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250958.2	1	0	0	14	252	0	58	0	7.016222e-01	0	45	0	58	2		0	0	0	0	0	2	1	0.999758	14	249	0	57	2		0	0	0	0	58	2	-3.220504	1	1	0	0		1	2	2	4	2.130453	1	0.240000	3.280000	0.384715	0.550000	0.310000	0.920000	0.530000	0.576502	0.550000	0	4.200000e-01	7.200000e-01
MAGI2	9863	broad.mit.edu	37	7	77755148	77755148	+	Missense_Mutation	SNP	C	C	A			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr7:77755148C>A	ENST00000354212.4	-	20	3683	c.3430G>T	c.(3430-3432)Gat>Tat	p.D1144Y	MAGI2_ENST00000419488.1_Missense_Mutation_p.D1130Y|MAGI2_ENST00000522391.1_Missense_Mutation_p.D1144Y	NM_012301.3	NP_036433.2	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 2			84		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)			GTGAAATAATCAAAATCCTTT	0.398000																								0							SO:0001583	missense			ENST00000354212.4	0	1	hg19	CCDS5594.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.826992	0.90955	.	.	ENSG00000187391	ENST00000419488;ENST00000354212;ENST00000536298;ENST00000522391	T;T;T	0.17691	2.26;2.26;2.26	6.03	6.03	0.97812	PDZ/DHR/GLGF (1);	0.000000	0.37530	U	0.002049	T	0.33498	0.0865	L	0.27053	0.805	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.85130	0.997;0.994;0.997	T	0.03175	-1.1064	10	0.72032	D	0.01	.	20.5568	0.99304	0.0:1.0:0.0:0.0	.	1144;1130;1144	E7EWI0;Q86UL8-2;Q86UL8	.;.;MAGI2_HUMAN	Y	1130;1144;1144;1144	ENSP00000405766:D1130Y;ENSP00000346151:D1144Y;ENSP00000428389:D1144Y	ENSP00000346151:D1144Y	D	-	1	0	MAGI2	77593084	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.818000	0.86416	2.861000	0.98227	0.655000	0.94253	GAT		TCGA-YB-A89D-01A-12D-A36O-08	MAGI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253197.3	0	0	0	13	453	0	70	0	1.304713e-02	0	6	0	70	2		0	0	0	0	0	2	1	0.999512	14	447	0	69	2		0	0	0	0	70	2	-3.286784	1	1	0	0		1	2	2	4	2.150457	1	0.240000	3.280000	0.387097	0.290000	0.160000	0.470000	0.280000	0.308075	0.290000	0	2.200000e-01	3.900000e-01
SLC25A40	55972	broad.mit.edu	37	7	87465581	87465581	+	Silent	SNP	G	G	T			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr7:87465581G>T	ENST00000341119.5	-	12	1346	c.1000C>A	c.(1000-1002)Cga>Aga	p.R334R		NM_018843.3	NP_061331.2	Q8TBP6	S2540_HUMAN	solute carrier family 25, member 40			17	Esophageal squamous(14;0.00202)				TGCTGCCTTCGAACATTTTGT	0.373000																								0							SO:0001819	synonymous_variant			ENST00000341119.5	1	0	hg19	CCDS5610.1																																																																																				TCGA-YB-A89D-01A-12D-A36O-08	SLC25A40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253677.5	1	0	0	14	333	0	45	0	1.517254e-01	0	16	0	45	2		0	0	0	0	0	2	1	0.999738	13	328	0	44	2		0	0	0	0	45	2	-2.956587	1	1	0	0		1	2	2	4	2.150457	1	0.240000	3.280000	0.387097	0.420000	0.240000	0.670000	0.410000	0.442112	0.420000	0	3.200000e-01	5.500000e-01
SLC25A13	10165	broad.mit.edu	37	7	95813702	95813702	+	Missense_Mutation	SNP	C	C	T			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr7:95813702C>T	ENST00000265631.5	-	11	1200	c.1064G>A	c.(1063-1065)cGa>cAa	p.R355Q	SLC25A13_ENST00000542654.1_Missense_Mutation_p.R247Q|SLC25A13_ENST00000416240.2_Missense_Mutation_p.R356Q			Q9UJS0	CMC2_HUMAN	solute carrier family 25 (aspartate/glutamate carrier), member 13			42	all_cancers(62;7.75e-08)|all_epithelial(64;1.16e-07)		STAD - Stomach adenocarcinoma(171;0.194)	L-Aspartic Acid(DB00128)	GTTCTGCATTCGAGTTTTTAC	0.373000																								0							SO:0001583	missense			ENST00000265631.5	1	1	hg19	CCDS5645.1	.	.	.	.	.	.	.	.	.	.	C	28.8	4.952987	0.92660	.	.	ENSG00000004864	ENST00000265631;ENST00000416240;ENST00000542654	D;D;D	0.83591	-1.74;-1.74;-1.74	4.56	3.68	0.42216	Mitochondrial carrier domain (2);	0.000000	0.64402	D	0.000001	D	0.90728	0.7090	M	0.83774	2.66	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.995;0.997;0.997	D	0.91822	0.5468	10	0.87932	D	0	-7.7694	12.8922	0.58078	0.0:0.9209:0.0:0.0791	.	247;356;355	F5GX33;Q546F9;Q9UJS0	.;.;CMC2_HUMAN	Q	355;356;247	ENSP00000265631:R355Q;ENSP00000400101:R356Q;ENSP00000440484:R247Q	ENSP00000265631:R355Q	R	-	2	0	SLC25A13	95651638	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.651000	0.83577	1.279000	0.44446	0.655000	0.94253	CGA		TCGA-YB-A89D-01A-12D-A36O-08	SLC25A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059395.2	1	0	1	66	262	0	45	1	9.969872e-01	13	25	0	45	2		0	0	0	0	0	2	1	1.000000	65	259	0	44	2		0	0	0	0	45	2	-3.562770	1	1	121410	1	36	1	2	2	4	2.150457	1	0.240000	3.280000	0.387097	0.990000	0.990000	1.000000	1.000000	1.000000	0.990000	1	9.900000e-01	1
SLC25A13	10165	broad.mit.edu	37	7	95818680	95818680	+	Missense_Mutation	SNP	A	A	C			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr7:95818680A>C	ENST00000265631.5	-	9	995	c.859T>G	c.(859-861)Tta>Gta	p.L287V	SLC25A13_ENST00000542654.1_Missense_Mutation_p.L179V|SLC25A13_ENST00000416240.2_Missense_Mutation_p.L287V			Q9UJS0	CMC2_HUMAN	solute carrier family 25 (aspartate/glutamate carrier), member 13			42	all_cancers(62;7.75e-08)|all_epithelial(64;1.16e-07)		STAD - Stomach adenocarcinoma(171;0.194)	L-Aspartic Acid(DB00128)	ATGTCTGCTAAGGTCATACGT	0.393000																								0							SO:0001583	missense			ENST00000265631.5	1	1	hg19	CCDS5645.1	.	.	.	.	.	.	.	.	.	.	A	8.292	0.818007	0.16607	.	.	ENSG00000004864	ENST00000265631;ENST00000416240;ENST00000542654	T;T;T	0.80653	-1.4;-1.39;-1.37	4.69	3.55	0.40652	EF-hand-like domain (1);	.	.	.	.	T	0.79678	0.4487	M	0.83223	2.63	0.42021	D	0.990984	B;B;B	0.25206	0.12;0.073;0.073	B;B;B	0.28916	0.096;0.044;0.044	T	0.76326	-0.3000	9	0.42905	T	0.14	-8.2043	6.7603	0.23536	0.7888:0.0:0.0753:0.1359	.	179;287;287	F5GX33;Q546F9;Q9UJS0	.;.;CMC2_HUMAN	V	287;287;179	ENSP00000265631:L287V;ENSP00000400101:L287V;ENSP00000440484:L179V	ENSP00000265631:L287V	L	-	1	2	SLC25A13	95656616	0.324000	0.24652	1.000000	0.80357	0.164000	0.22412	1.072000	0.30678	1.129000	0.42072	0.533000	0.62120	TTA		TCGA-YB-A89D-01A-12D-A36O-08	SLC25A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059395.2	0	0	0	13	316	0	48	1	4.176262e-01	2	32	0	48	2		0	0	0	0	0	2	1	0.999532	13	313	0	48	2		0	0	0	0	48	2	-14.012840	1	1	0	0		1	2	2	4	2.150457	1	0.240000	3.280000	0.387097	0.410000	0.230000	0.660000	0.400000	0.434968	0.410000	0	3.100000e-01	5.400000e-01
CSMD3	114788	broad.mit.edu	37	8	113256691	113256691	+	Missense_Mutation	SNP	G	G	A			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr8:113256691G>A	ENST00000297405.5	-	65	10578	c.10334C>T	c.(10333-10335)gCa>gTa	p.A3445V	CSMD3_ENST00000352409.3_Missense_Mutation_p.A3375V|CSMD3_ENST00000455883.2_Missense_Mutation_p.A3276V|CSMD3_ENST00000343508.3_Missense_Mutation_p.A3405V	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	p.A3445V(1)		646					TGTTCCACCTGCTAAGAAGAA	0.423000										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)														1	Substitution - Missense(1)						SO:0001583	missense			ENST00000297405.5	1	1	hg19	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.522882	0.85600	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.62364	0.03;0.03;0.03;0.03;0.03	5.37	4.5	0.54988	Complement control module (2);Sushi/SCR/CCP (3);	0.171297	0.39615	N	0.001317	T	0.55800	0.1943	N	0.10618	0.005	0.43896	D	0.996523	P;P;D	0.58970	0.532;0.65;0.984	B;B;P	0.59171	0.356;0.428;0.853	T	0.56768	-0.7924	10	0.25106	T	0.35	.	14.1728	0.65522	0.0714:0.0:0.9286:0.0	.	3276;3445;3405	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	V	3405;3445;2715;3276;3375	ENSP00000345799:A3405V;ENSP00000297405:A3445V;ENSP00000341558:A2715V;ENSP00000412263:A3276V;ENSP00000343124:A3375V	ENSP00000297405:A3445V	A	-	2	0	CSMD3	113325867	1.000000	0.71417	1.000000	0.80357	0.864000	0.49448	7.554000	0.82212	1.508000	0.48769	-0.229000	0.12294	GCA		TCGA-YB-A89D-01A-12D-A36O-08	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	1	0	1	52	451	0	90		0	0	0	0	90	2		0	0	0	0	0	2	1	1.000000	50	445	0	89	2		0	0	0	0	90	2	-17.324610	1	1	0	0		1	2	2	4	2.144854	1	0.240000	3.280000	0.387097	0.990000	0.810000	1.000000	1.000000	0.976244	0.990000	1	9.300000e-01	1
COL14A1	7373	broad.mit.edu	37	8	121160132	121160132	+	Missense_Mutation	SNP	G	G	T			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr8:121160132G>T	ENST00000297848.3	+	2	321	c.51G>T	c.(49-51)ttG>ttT	p.L17F	COL14A1_ENST00000537875.1_Missense_Mutation_p.L17F|COL14A1_ENST00000247781.3_Missense_Mutation_p.L17F|COL14A1_ENST00000309791.4_Missense_Mutation_p.L17F|COL14A1_ENST00000432943.2_3'UTR	NM_021110.1	NP_066933.1			collagen, type XIV, alpha 1			119	Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503)		CACCTTTTTTGGCAATTGTTT	0.408000																								0							SO:0001583	missense			ENST00000297848.3	0	1	hg19	CCDS34938.1	.	.	.	.	.	.	.	.	.	.	G	9.500	1.102890	0.20632	.	.	ENSG00000187955	ENST00000537875;ENST00000309791;ENST00000297848;ENST00000247781	T;D;D;D	0.88896	0.4;-2.23;-2.26;-2.44	5.92	5.04	0.67666	.	0.680937	0.13024	N	0.419846	D	0.82683	0.5090	N	0.24115	0.695	0.20563	N	0.999883	B	0.02656	0.0	B	0.04013	0.001	T	0.73927	-0.3828	10	0.66056	D	0.02	.	12.49	0.55895	0.0:0.0:0.8328:0.1672	.	17	Q05707	COEA1_HUMAN	F	17	ENSP00000443974:L17F;ENSP00000311809:L17F;ENSP00000297848:L17F;ENSP00000247781:L17F	ENSP00000247781:L17F	L	+	3	2	COL14A1	121229313	0.226000	0.23696	0.731000	0.30826	0.189000	0.23516	1.973000	0.40550	1.505000	0.48720	0.655000	0.94253	TTG		TCGA-YB-A89D-01A-12D-A36O-08	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313657.2	0	0	0	8	426	0	89	0	3.606061e-01	0	62	0	89	2		0	0	0	0	0	2	1	0.988896	8	420	0	89	2		0	0	0	0	89	2	-4.344852	1	1	0	0		1	2	2	4	2.144854	1	0.240000	3.280000	0.387097	0.190000	0.080000	0.360000	0.200000	0.212530	0.190000	0	1.300000e-01	2.800000e-01
RP1	6101	broad.mit.edu	37	8	55539537	55539537	+	Missense_Mutation	SNP	A	A	G			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr8:55539537A>G	ENST00000220676.1	+	4	3243	c.3095A>G	c.(3094-3096)aAt>aGt	p.N1032S		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)			169		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)		TCAGCTATTAATGATCATAAT	0.378000													Colon(91;1014 1389 7634 14542 40420)											0							SO:0001583	missense			ENST00000220676.1	1	1	hg19	CCDS6160.1	.	.	.	.	.	.	.	.	.	.	A	2.654	-0.281375	0.05642	.	.	ENSG00000104237	ENST00000220676	T	0.20881	2.04	5.32	1.41	0.22369	.	0.779574	0.11892	N	0.519542	T	0.08891	0.0220	N	0.04959	-0.14	0.09310	N	1	B	0.14805	0.011	B	0.15870	0.014	T	0.29150	-1.0021	10	0.41790	T	0.15	.	3.9076	0.09190	0.5898:0.0:0.2595:0.1508	.	1032	P56715	RP1_HUMAN	S	1032	ENSP00000220676:N1032S	ENSP00000220676:N1032S	N	+	2	0	RP1	55702090	0.000000	0.05858	0.006000	0.13384	0.072000	0.16883	-0.139000	0.10358	0.435000	0.26365	0.533000	0.62120	AAT		TCGA-YB-A89D-01A-12D-A36O-08	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	1	0	1	211	784	0	196		0	0	0	0	196	2		0	0	0	0	0	2	1	1.000000	208	776	0	195	2		0	0	0	0	196	2	-20.000000	1	1	0	0		1	2	2	4	2.144854	1	0.240000	3.280000	0.387097	0.990000	0.990000	1.000000	1.000000	1.000000	0.990000	1	9.900000e-01	1
NBN	4683	broad.mit.edu	37	8	90965576	90965576	+	Missense_Mutation	SNP	G	G	T			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr8:90965576G>T	ENST00000265433.3	-	11	1895	c.1741C>A	c.(1741-1743)Caa>Aaa	p.Q581K	NBN_ENST00000409330.1_Missense_Mutation_p.Q499K	NM_002485.4	NP_002476.2	O60934	NBN_HUMAN	nibrin			27			BRCA - Breast invasive adenocarcinoma(11;0.0344)		TCCTGTTTTTGAACTTTCACA	0.348000								Homologous recombination																0							SO:0001583	missense			ENST00000265433.3	0	1	hg19	CCDS6249.1	.	.	.	.	.	.	.	.	.	.	G	7.975	0.749994	0.15778	.	.	ENSG00000104320	ENST00000265433;ENST00000409330	T;T	0.58060	1.99;0.36	5.29	0.895	0.19247	.	1.667470	0.02817	N	0.125095	T	0.38026	0.1025	N	0.19112	0.55	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.17349	-1.0372	10	0.12766	T	0.61	-0.018	9.8904	0.41288	0.0:0.5366:0.322:0.1413	.	581;581	A6H8Y5;O60934	.;NBN_HUMAN	K	581;499	ENSP00000265433:Q581K;ENSP00000386924:Q499K	ENSP00000265433:Q581K	Q	-	1	0	NBN	91034752	0.001000	0.12720	0.261000	0.24466	0.911000	0.54048	0.129000	0.15830	0.139000	0.18822	0.650000	0.86243	CAA		TCGA-YB-A89D-01A-12D-A36O-08	NBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331583.3	0	0	0	18	832	0	157	0	3.753665e-01	0	59	0	157	2		0	0	0	0	0	2	1	0.999980	17	825	0	156	2		0	0	0	0	157	2	-2.506821	1	1	0	0		1	2	2	4	2.144854	1	0.240000	3.280000	0.387097	0.220000	0.120000	0.340000	0.210000	0.230014	0.220000	0	1.700000e-01	2.800000e-01
SLC26A7	115111	broad.mit.edu	37	8	92365218	92365218	+	Silent	SNP	C	C	A			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr8:92365218C>A	ENST00000276609.3	+	11	1547	c.1308C>A	c.(1306-1308)atC>atA	p.I436I	SLC26A7_ENST00000520249.1_3'UTR|SLC26A7_ENST00000523719.1_Silent_p.I436I|SLC26A7_ENST00000309536.2_Silent_p.I436I	NM_001282356.1|NM_052832.2	NP_001269285.1|NP_439897.1			solute carrier family 26 (anion exchanger), member 7			50			BRCA - Breast invasive adenocarcinoma(11;0.00802)		TGGATAAAATCGATTGGGTAA	0.308000																								0							SO:0001819	synonymous_variant			ENST00000276609.3	1	0	hg19	CCDS6254.1																																																																																				TCGA-YB-A89D-01A-12D-A36O-08	SLC26A7-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377011.1	1	0	0	19	486	0	76		0	0	0	0	76	2		0	0	0	0	0	2	1	0.999990	18	481	0	75	2		0	0	0	0	76	2	-3.801436	1	1	0	0		1	2	2	4	2.144854	1	0.240000	3.280000	0.387097	0.390000	0.240000	0.580000	0.400000	0.406359	0.390000	0	3.100000e-01	4.900000e-01
MTERFD1	0	broad.mit.edu	37	8	97263135	97263135	+	Splice_Site	SNP	T	T	A			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr8:97263135T>A	ENST00000287025.3	-	4	774	c.676A>T	c.(676-678)Agg>Tgg	p.R226W	MTERFD1_ENST00000522822.1_Splice_Site_p.R105W|MTERFD1_ENST00000523821.1_Splice_Site_p.R226W|MTERFD1_ENST00000524341.1_Splice_Site_p.R36W	NM_015942.3	NP_057026.3	Q96E29	MTEF3_HUMAN				24	Breast(36;5.16e-05)				AAGTCCTACCTGGTCTTCAGA	0.368000																								0							SO:0001630	splice_region_variant			ENST00000287025.3	1	0	hg19	CCDS6270.1	.	.	.	.	.	.	.	.	.	.	T	18.18	3.566661	0.65651	.	.	ENSG00000156469	ENST00000523821;ENST00000522822;ENST00000524341;ENST00000287025	T;T;T;T	0.11712	2.75;2.75;2.75;2.75	5.72	5.72	0.89469	.	0.090695	0.85682	D	0.000000	T	0.38054	0.1026	M	0.87180	2.865	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.26883	-1.0090	10	0.40728	T	0.16	-6.2986	14.5668	0.68182	0.0:0.0:0.0:1.0	.	226;226	E5RIK9;Q96E29	.;MTER1_HUMAN	W	226;105;36;226	ENSP00000429400:R226W;ENSP00000430138:R105W;ENSP00000429267:R36W;ENSP00000287025:R226W	ENSP00000287025:R226W	R	-	1	2	MTERFD1	97332311	1.000000	0.71417	0.997000	0.53966	0.291000	0.27294	5.366000	0.66122	2.172000	0.68678	0.482000	0.46254	AGG		TCGA-YB-A89D-01A-12D-A36O-08	MTERFD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379876.1	1	0	1	96	402	0	86	0	9.507138e-01	1	22	0	86	2		0	0	0	0	0	2	1	1.000000	96	395	0	85	2		0	0	0	0	86	2	-20.000000	1	1	0	0		1	2	2	4	2.144854	1	0.240000	3.280000	0.387097	0.990000	0.990000	1.000000	1.000000	1.000000	0.990000	1	9.900000e-01	1
POP1	10940	broad.mit.edu	37	8	99142441	99142441	+	Missense_Mutation	SNP	G	G	A	rs148502433	byFrequency	TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr8:99142441G>A	ENST00000401707.2	+	5	803	c.722G>A	c.(721-723)cGg>cAg	p.R241Q	POP1_ENST00000349693.3_Missense_Mutation_p.R241Q	NM_001145860.1|NM_001145861.1	NP_001139332.1|NP_001139333.1	Q99575	POP1_HUMAN	processing of precursor 1, ribonuclease P/MRP subunit (S. cerevisiae)			36	Breast(36;1.78e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.145)		ATGACGAACCGGTGCCTCCTG	0.498000																								0							SO:0001583	missense			ENST00000401707.2	0	1	hg19	CCDS6277.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	10.70	1.424994	0.25639	0.0	2.33E-4	ENSG00000104356	ENST00000401707;ENST00000349693	T;T	0.41758	0.99;0.99	5.91	-1.73	0.08081	Ribonuclease P/MRP, subunit POP1 (1);	0.441265	0.23766	N	0.044766	T	0.20170	0.0485	L	0.28400	0.85	0.09310	N	1	B	0.22851	0.076	B	0.22753	0.041	T	0.06917	-1.0800	9	.	.	.	-14.9496	0.3734	0.00383	0.3481:0.131:0.2675:0.2534	.	241	Q99575	POP1_HUMAN	Q	241	ENSP00000385787:R241Q;ENSP00000339529:R241Q	.	R	+	2	0	POP1	99211617	0.044000	0.20184	0.001000	0.08648	0.221000	0.24807	1.582000	0.36568	-0.185000	0.10550	-0.176000	0.13171	CGG		TCGA-YB-A89D-01A-12D-A36O-08	POP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379470.1	0	0	0	7	559	0	101	0	2.143319e-03	0	5	0	101	2		0	0	0	0	0	2	1	0.978498	7	542	0	95	2		0	0	0	0	101	2	-2.641306	1	1	121410	25	47	1	2	2	4	2.144854	1	0.240000	3.280000	0.387097	0.130000	0.050000	0.250000	0.120000	0.145174	0.130000	0	8.000000e-02	2.000000e-01
ZNF462	58499	broad.mit.edu	37	9	109688806	109688806	+	Missense_Mutation	SNP	C	C	A			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr9:109688806C>A	ENST00000277225.5	+	3	2902	c.2613C>A	c.(2611-2613)ttC>ttA	p.F871L	ZNF462_ENST00000441147.2_5'Flank|ZNF462_ENST00000457913.1_Missense_Mutation_p.F871L			Q96JM2	ZN462_HUMAN	zinc finger protein 462			119					ACATTAAATTCAGCTTTAGGT	0.443000																								0							SO:0001583	missense			ENST00000277225.5	0	1	hg19	CCDS35096.1	.	.	.	.	.	.	.	.	.	.	C	17.66	3.443804	0.63067	.	.	ENSG00000148143	ENST00000277225;ENST00000457913	T;T	0.11385	2.78;3.18	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	T	0.14356	0.0347	N	0.08118	0	0.80722	D	1	D;D	0.63880	0.992;0.993	D;D	0.74674	0.984;0.956	T	0.33445	-0.9868	9	.	.	.	.	13.2624	0.60113	0.0:0.9279:0.0:0.072	.	871;871	Q96JM2-3;Q96JM2	.;ZN462_HUMAN	L	871	ENSP00000277225:F871L;ENSP00000414570:F871L	.	F	+	3	2	ZNF462	108728627	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.499000	0.35671	2.731000	0.93534	0.650000	0.86243	TTC		TCGA-YB-A89D-01A-12D-A36O-08	ZNF462-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053532.2	0	0	0	19	849	0	218	0	5.517198e-04	0	2	0	218	2		0	0	0	0	0	2	1	0.999989	19	841	0	216	2		0	0	0	0	218	2	-2.707120	1	1	0	0		1	1	2	3	1.937552	0	0.240000	3.280000	0.320701	0.200000	0.120000	0.320000	0.210000	0.213807	0.200000	0	1.600000e-01	2.600000e-01
RAB14	51552	broad.mit.edu	37	9	123952957	123952957	+	Silent	SNP	G	G	T			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr9:123952957G>T	ENST00000373840.4	-	4	396	c.159C>A	c.(157-159)atC>atA	p.I53I		NM_016322.3	NP_057406.2	P61106	RAB14_HUMAN	RAB14, member RAS oncogene family			5					CACTAACTTCGATTATTCTTG	0.418000																								0							SO:0001819	synonymous_variant			ENST00000373840.4	1	0	hg19	CCDS6827.1																																																																																				TCGA-YB-A89D-01A-12D-A36O-08	RAB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053857.1	1	0	0	19	384	0	70	0	9.785283e-01	0	129	0	70	2		0	0	0	0	0	2	1	0.999990	19	377	0	68	2		0	0	0	0	70	2	-4.810085	1	0	0	0		1	1	2	3	1.931108	0	0.240000	3.280000	0.319971	0.440000	0.270000	0.700000	0.440000	0.462812	0.440000	0	3.500000e-01	5.600000e-01
GRHPR	9380	broad.mit.edu	37	9	37425975	37425975	+	Missense_Mutation	SNP	G	G	A			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr9:37425975G>A	ENST00000318158.6	+	3	356	c.271G>A	c.(271-273)Gat>Aat	p.D91N	GRHPR_ENST00000493368.1_3'UTR|GRHPR_ENST00000607784.1_Missense_Mutation_p.D91N	NM_012203.1	NP_036335.1	Q9UBQ7	GRHPR_HUMAN	glyoxylate reductase/hydroxypyruvate reductase			12					CTTGGCTTTGGATGAAATCAA	0.488000																								0							SO:0001583	missense			ENST00000318158.6	1	0	hg19	CCDS6609.1	.	.	.	.	.	.	.	.	.	.	G	19.81	3.896202	0.72639	.	.	ENSG00000137106	ENST00000377824;ENST00000318158	D;D	0.85088	-1.94;-1.94	5.72	5.72	0.89469	D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain (1);NAD(P)-binding domain (1);	0.238434	0.47455	D	0.000233	T	0.81856	0.4911	L	0.39147	1.195	0.58432	D	0.999999	B;B;B	0.14805	0.011;0.0;0.0	B;B;B	0.21546	0.035;0.004;0.004	T	0.75448	-0.3314	10	0.35671	T	0.21	-15.1581	18.5201	0.90948	0.0:0.0:1.0:0.0	.	91;91;91	Q5T946;Q5T945;Q9UBQ7	.;.;GRHPR_HUMAN	N	91	ENSP00000367055:D91N;ENSP00000313432:D91N	ENSP00000313432:D91N	D	+	1	0	GRHPR	37415975	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.338000	0.79269	2.708000	0.92522	0.650000	0.86243	GAT		TCGA-YB-A89D-01A-12D-A36O-08	GRHPR-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052442.1	1	0	0	24	268	0	58	1	9.999974e-01	3	236	0	58	2		0	0	0	0	0	2	1	1.000000	18	266	0	56	2		0	0	0	0	58	2	-20.000000	1	1	0	0		1						0.240000	3.280000									0	0
ZCCHC6	79670	broad.mit.edu	37	9	88953781	88953781	+	Missense_Mutation	SNP	G	G	T			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr9:88953781G>T	ENST00000375963.3	-	9	1464	c.1292C>A	c.(1291-1293)cCa>cAa	p.P431Q	ZCCHC6_ENST00000375961.2_Missense_Mutation_p.P431Q|ZCCHC6_ENST00000375960.2_Intron|ZCCHC6_ENST00000277141.6_5'UTR|ZCCHC6_ENST00000375948.1_Missense_Mutation_p.P69Q	NM_001185059.1|NM_024617.3	NP_001171988.1|NP_078893.2	Q5VYS8	TUT7_HUMAN	zinc finger, CCHC domain containing 6			46					AACCAGCTTTGGTTCTAGTTT	0.428000																								0							SO:0001583	missense			ENST00000375963.3	0	1	hg19	CCDS35057.1	.	.	.	.	.	.	.	.	.	.	G	27.1	4.802284	0.90538	.	.	ENSG00000083223	ENST00000375961;ENST00000375963;ENST00000375948	T;T;T	0.73681	-0.77;-0.77;-0.77	4.56	4.56	0.56223	.	0.117764	0.64402	D	0.000017	D	0.84451	0.5475	M	0.77712	2.385	0.51482	D	0.999928	P;P	0.51653	0.947;0.891	P;P	0.58331	0.837;0.617	D	0.86390	0.1735	10	0.59425	D	0.04	-16.5782	17.8715	0.88812	0.0:0.0:1.0:0.0	.	431;431	Q5VYS8-2;Q5VYS8	.;TUT7_HUMAN	Q	431;431;69	ENSP00000365128:P431Q;ENSP00000365130:P431Q;ENSP00000365115:P69Q	ENSP00000365115:P69Q	P	-	2	0	ZCCHC6	88143601	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.788000	0.69020	2.520000	0.84964	0.655000	0.94253	CCA		TCGA-YB-A89D-01A-12D-A36O-08	ZCCHC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052918.1	0	0	0	8	420	0	84	0	6.237576e-02	0	19	0	84	2		0	0	0	0	0	2	1	0.988341	7	411	0	83	2		0	0	0	0	84	2	-3.195965	1	1	0	0		1	1	2	3	1.937552	0	0.240000	3.280000	0.320701	0.180000	0.080000	0.340000	0.180000	0.194175	0.180000	0	1.200000e-01	2.600000e-01
ASPN	54829	broad.mit.edu	37	9	95232987	95232987	+	Silent	SNP	G	G	T			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chr9:95232987G>T	ENST00000375544.3	-	3	594	c.351C>A	c.(349-351)atC>atA	p.I117I	ASPN_ENST00000395538.3_Silent_p.I117I|CENPP_ENST00000375587.3_Intron|ASPN_ENST00000375543.1_Silent_p.I117I	NM_017680.4	NP_060150	Q9BXN1	ASPN_HUMAN	asporin			9					CATTTTCTTTGATTTCCTTAA	0.289000																								0							SO:0001819	synonymous_variant			ENST00000375544.3	0	1	hg19																																																																																					TCGA-YB-A89D-01A-12D-A36O-08	ASPN-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000053094.1	0	0	0	14	543	0	100	0	9.256721e-01	0	175	0	100	2		0	0	0	0	0	2	1	0.999732	14	535	0	99	2		0	0	0	0	100	2	-3.229789	1	1	0	0		1	1	2	3	1.937552	0	0.240000	3.280000	0.320701	0.230000	0.130000	0.390000	0.240000	0.249230	0.230000	0	1.800000e-01	3.100000e-01
RPS6KA6	27330	broad.mit.edu	37	X	83372157	83372157	+	Splice_Site	SNP	C	C	A			TCGA-YB-A89D-01A-12D-A36O-08	TCGA-YB-A89D-10A-01D-A367-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be60a8c7-3037-4c1a-9629-ef98e567b338	82dc60fa-8b94-4c7b-bbf4-39e0118a77d8	g.chrX:83372157C>A	ENST00000262752.2	-	11	868		c.e11-1		RPS6KA6_ENST00000543399.1_Splice_Site	NM_014496.4	NP_055311.1	Q9UK32	KS6A6_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 6			46					AAGTTTTGCTCTGAAACAGAG	0.323000																								0							SO:0001630	splice_region_variant			ENST00000262752.2	0	1	hg19	CCDS14451.1	.	.	.	.	.	.	.	.	.	.	C	19.66	3.869083	0.72065	.	.	ENSG00000072133	ENST00000262752;ENST00000543399	.	.	.	4.64	4.64	0.57946	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.0306	0.86460	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	RPS6KA6	83258813	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	7.552000	0.82192	2.028000	0.59812	0.600000	0.82982	.		TCGA-YB-A89D-01A-12D-A36O-08	RPS6KA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057372.1	0	0	0	6	221	0	36		0	0	0	0	36	2		0	0	0	0	0	2	1	0.963101	6	216	0	36	2		0	0	0	0	36	2	-3.292772	1	1	0	0		1	0	1	1			0.240000	3.280000	0.240000	0.110000	0.040000	0.220000	0.110000	0.125589	0.110000	0	7.000000e-02	1.700000e-01
