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
BRAF	673	broad.mit.edu	37	7	140477837	140477851	+	In_Frame_Del	DEL	TAGGTGCTGTCACAT	TAGGTGCTGTCACAT	-			TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr7:140477837_140477851delTAGGTGCTGTCACAT	ENST00000288602.6	-	12	1517_1531	c.1457_1471delATGTGACAGCACCTA	c.(1456-1473)aatgtgacagcacctaca>aca	p.NVTAP486del		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	p.L485_P490>Y(2)|p.N486_P490del(1)	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	27380	Melanoma(164;0.00956)			Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	TGCTGAGGTGTAGGTGCTGTCACATTCAACATTTT	0.349000		61	Mis, T, O	AKAP9, KIAA1549	melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous syndrome				Colon(40;35 892 2973 5743 27438)		Dom	yes		7	7q34	673	v-raf murine sarcoma viral oncogene homolog B1	yes	E	3	Complex - deletion inframe(2)|Deletion - In frame(1)	GRCh37	CM071573	BRAF	M		SO:0001651	inframe_deletion	Familial Cancer Database	CFC, CFCS	ENST00000288602.6	0	1	hg19	CCDS5863.1																																																																																				TCGA-IB-A5SQ-01A-11D-A32N-08	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	0	0	0	10	332	0	63	0	6.612028e-02	0	13	0	63	2	0	0	0	0	0	0		1	0.997481	16	338	0	64	2	0	0	0	0	0	0		-3.661989	1	1	0	0		1	1	2	3	2.035490	0	0.150000	1.900000	0.157582	0.420000	0.210000	1.000000	0.390000	0.479202	0.420000	0	0.300000	0.620000
RDX	5962	broad.mit.edu	37	11	110108327	110108327	+	Nonsense_Mutation	SNP	G	G	A			TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08			G	A	G	G		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr11:110108327G>A	ENST00000343115.4	-	11	1460	c.1141C>T	c.(1141-1143)Cga>Tga	p.R381*	RDX_ENST00000544551.1_Nonsense_Mutation_p.R245*|RDX_ENST00000405097.1_Nonsense_Mutation_p.R381*|RDX_ENST00000528498.1_Nonsense_Mutation_p.R381*|RDX_ENST00000530301.1_Intron|RDX_ENST00000528900.1_Nonsense_Mutation_p.R34*	NM_001260494.1|NM_002906.3	NP_001247423.1|NP_002897.1	P35241	RADI_HUMAN	radixin			18		all_cancers(61;7.18e-13)|all_epithelial(67;2.61e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)			TCTTTTGCTCGTTTTCGTTCT	0.428000													Esophageal Squamous(55;25 1062 11040 28755 44273)											0							SO:0001587	stop_gained			ENST00000343115.4	0	1	hg19	CCDS8343.1	.	.	.	.	.	.	.	.	.	.	G	41	8.898136	0.98994	.	.	ENSG00000137710	ENST00000528498;ENST00000405097;ENST00000528900;ENST00000343115;ENST00000544551;ENST00000530085	.	.	.	5.78	4.84	0.62591	.	0.354723	0.25230	N	0.032165	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.12103	T	0.63	.	14.7001	0.69150	0.0:0.0:0.7205:0.2795	.	.	.	.	X	381;381;34;381;245;51	.	ENSP00000342830:R381X	R	-	1	2	RDX	109613537	0.998000	0.40836	1.000000	0.80357	0.998000	0.95712	1.566000	0.36396	1.364000	0.46038	0.650000	0.86243	CGA		TCGA-IB-A5SQ-01A-11D-A32N-08	RDX-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390535.2	1	0	0	34	424	0	93	0	9.951046e-01	0	104	0	93	2		0	0	0	0	0	2	1	1.000000	34	418	0	92	2	0	0	0	0	0	0		-8.919833	1	1	0	0		1	0	1	1	2.003944	1	0.150000	1.900000	0.081081	0.850000	0.620000	0.990000	0.890000	0.847335	0.850000	1	0.730000	0.950000
OR5F1	338674	broad.mit.edu	37	11	55761879	55761879	+	Missense_Mutation	SNP	T	T	G			TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr11:55761879T>G	ENST00000278409.1	-	1	222	c.223A>C	c.(223-225)Act>Cct	p.T75P		NM_003697.1	NP_003688.1	O95221	OR5F1_HUMAN	olfactory receptor, family 5, subfamily F, member 1			58	Esophageal squamous(21;0.00448)				GTGATGGTAGTTGAGTTACAA	0.443000																								0							SO:0001583	missense			ENST00000278409.1	1	1	hg19	CCDS31515.1	.	.	.	.	.	.	.	.	.	.	T	9.452	1.090942	0.20471	.	.	ENSG00000149133	ENST00000278409	T	0.00402	7.56	3.03	0.33	0.15929	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00468	0.0015	M	0.79926	2.475	0.09310	N	1	B	0.34226	0.443	B	0.32465	0.146	T	0.34900	-0.9810	9	0.87932	D	0	.	7.279	0.26300	0.4403:0.0:0.0:0.5596	.	75	O95221	OR5F1_HUMAN	P	75	ENSP00000278409:T75P	ENSP00000278409:T75P	T	-	1	0	OR5F1	55518455	0.006000	0.16342	0.036000	0.18154	0.077000	0.17291	0.070000	0.14573	-0.198000	0.10333	0.247000	0.18012	ACT		TCGA-IB-A5SQ-01A-11D-A32N-08	OR5F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391532.1	1	0	1	34	294	0	67		0	0	0	0	67	2		0	0	0	0	0	2	1	1.000000	33	293	0	67	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	0	1	1	1.862665	1	0.150000	1.900000	0.084791	0.970000	0.780000	1.000000	1.000000	0.955352	0.970000	1	0.890000	1.000000
SLC22A20	440044	broad.mit.edu	37	11	65004295	65004295	+	RNA	SNP	G	G	A			TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr11:65004295G>A	ENST00000525437.1	+	0	1545							A6NK97	S22AK_HUMAN	solute carrier family 22, member 20			8					TGGGCTGGCCGTCTGCGTCCT	0.657000																								0											ENST00000525437.1	0	1	hg19																																																																																					TCGA-IB-A5SQ-01A-11D-A32N-08	SLC22A20-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000385336.1	0	0	0	6	548	0	101		0	0	0	0	101	2		0	0	0	0	0	2	1	0.962697	6	537	0	100	2	0	0	0	0	0	0		-3.212343	1	1	121026	4	37	1	0	1	1	2.003944	1	0.150000	1.900000	0.081081	0.130000	0.050000	0.270000	0.130000	0.152098	0.130000	0	0.090000	0.210000
SYTL2	54843	broad.mit.edu	37	11	85468696	85468696	+	Silent	SNP	G	G	A			TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr11:85468696G>A	ENST00000528231.1	-	1	350	c.73C>T	c.(73-75)Ctg>Ttg	p.L25L	SYTL2_ENST00000527523.1_Intron|SYTL2_ENST00000524452.1_Silent_p.L25L|SYTL2_ENST00000389960.4_Silent_p.L25L|SYTL2_ENST00000316356.4_Silent_p.L25L	NM_001162951.1|NM_001162953.1	NP_001156423.1|NP_001156425.1	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2			52		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)			GCCCTCTTCAGAGCAGCATCC	0.478000																								0							SO:0001819	synonymous_variant			ENST00000528231.1	1	1	hg19	CCDS53688.1																																																																																				TCGA-IB-A5SQ-01A-11D-A32N-08	SYTL2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392192.1	1	0	0	114	1331	0	283	1	1.568600e-01	2	7	0	283	2		0	0	0	0	0	2	1	1.000000	112	1308	0	281	2	0	0	0	0	0	0		-19.989460	1	1	0	0		1	0	1	1	2.003944	1	0.150000	1.900000	0.081081	0.920000	0.790000	1.000000	0.970000	0.922377	0.920000	1	0.850000	0.980000
TAS2R50	259296	broad.mit.edu	37	12	11138881	11138881	+	Missense_Mutation	SNP	T	T	C			TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr12:11138881T>C	ENST00000506868.1	-	1	630	c.579A>G	c.(577-579)atA>atG	p.I193M	TAS2R14_ENST00000381852.4_Intron|PRR4_ENST00000536668.1_Intron	NM_176890.2	NP_795371.2	P59544	T2R50_HUMAN	taste receptor, type 2, member 50			17					TCAGAAAAGATATCAGGGACA	0.408000																								0							SO:0001583	missense			ENST00000506868.1	1	1	hg19	CCDS8638.1	.	.	.	.	.	.	.	.	.	.	T	11.88	1.770932	0.31320	.	.	ENSG00000212126	ENST00000506868	T	0.41065	1.01	2.19	-2.61	0.06171	.	2.272960	0.03713	U	0.250636	T	0.47432	0.1445	M	0.80028	2.48	0.09310	N	1	P	0.38535	0.635	B	0.42361	0.385	T	0.48980	-0.8986	10	0.72032	D	0.01	.	3.8053	0.08774	0.1852:0.0:0.3371:0.4777	.	193	P59544	T2R50_HUMAN	M	193	ENSP00000424040:I193M	ENSP00000424040:I193M	I	-	3	3	TAS2R50	11030148	0.000000	0.05858	0.000000	0.03702	0.283000	0.27025	-0.609000	0.05635	-0.349000	0.08274	0.260000	0.18958	ATA		TCGA-IB-A5SQ-01A-11D-A32N-08	TAS2R50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370192.2	1	0	0	30	457	0	74		0	0	0	0	74	2		0	0	0	0	0	2	1	1.000000	30	453	0	74	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	1	2	3	2.042590	0	0.150000	1.900000	0.159456	0.850000	0.580000	1.000000	1.000000	0.852566	0.850000	1	0.700000	1.000000
CCDC60	160777	broad.mit.edu	37	12	119909828	119909828	+	Missense_Mutation	SNP	G	G	A	rs144740799	byFrequency	TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr12:119909828G>A	ENST00000327554.2	+	3	665	c.200G>A	c.(199-201)cGt>cAt	p.R67H	CCDC60_ENST00000546345.1_3'UTR|RP11-768F21.1_ENST00000509470.2_lincRNA	NM_178499.3	NP_848594.2	Q8IWA6	CCD60_HUMAN	coiled-coil domain containing 60			40	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)				AAGATAGGCCGTGGATATTTT	0.468000																								0							SO:0001583	missense			ENST00000327554.2	1	0	hg19	CCDS9190.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	10.93	1.490322	0.26686	9.08E-4	0.001977	ENSG00000183273	ENST00000327554	T	0.25912	1.77	5.22	2.0	0.26442	.	0.253027	0.26556	N	0.023712	T	0.39279	0.1072	M	0.68317	2.08	0.39642	D	0.970335	D	0.76494	0.999	D	0.64687	0.928	T	0.20107	-1.0285	9	.	.	.	-12.1971	5.4573	0.16598	0.399:0.0:0.601:0.0	.	67	Q8IWA6	CCD60_HUMAN	H	67	ENSP00000333374:R67H	.	R	+	2	0	CCDC60	118394211	0.438000	0.25602	0.512000	0.27736	0.025000	0.11179	0.906000	0.28517	0.593000	0.29745	-1.175000	0.01729	CGT		TCGA-IB-A5SQ-01A-11D-A32N-08	CCDC60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401680.1	1	0	0	21	400	0	84		0	0	0	0	84	2		0	0	0	0	0	2	1	0.999997	22	394	0	84	2	0	0	0	0	0	0		-4.790068	1	1	121412	195	55	1	0	1	1	1.897148	1	0.150000	1.900000	0.090666	0.610000	0.390000	0.890000	0.600000	0.632231	0.610000	0	0.490000	0.760000
GCN1L1	10985	broad.mit.edu	37	12	120602186	120602186	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr12:120602186G>A	ENST00000300648.6	-	18	1814	c.1802C>T	c.(1801-1803)gCg>gTg	p.A601V		NM_006836.1	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis 1-like 1 (yeast)			94	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)				GAGTCCGTGCGCCAGCTTAAA	0.612000																								0							SO:0001583	missense			ENST00000300648.6	0	1	hg19	CCDS41847.1	.	.	.	.	.	.	.	.	.	.	G	18.86	3.713573	0.68730	0.0	1.2E-4	ENSG00000089154	ENST00000300648	T	0.04654	3.58	5.83	5.83	0.93111	Armadillo-like helical (1);Domain of unknown function DUF3554 (1);Armadillo-type fold (1);	0.052807	0.85682	D	0.000000	T	0.05640	0.0148	L	0.49455	1.56	0.80722	D	1	B	0.29766	0.256	B	0.25291	0.059	T	0.39187	-0.9626	10	0.12103	T	0.63	.	13.3273	0.60467	0.0717:0.0:0.9283:0.0	.	601	Q92616	GCN1L_HUMAN	V	601	ENSP00000300648:A601V	ENSP00000300648:A601V	A	-	2	0	GCN1L1	119086569	1.000000	0.71417	0.965000	0.40720	0.937000	0.57800	7.375000	0.79646	2.769000	0.95229	0.655000	0.94253	GCG		TCGA-IB-A5SQ-01A-11D-A32N-08	GCN1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403592.1	0	0	0	6	642	0	127	0	6.702748e-03	0	11	0	127	2		0	0	0	0	0	2	1	0.963372	7	631	0	126	2	0	0	0	0	0	0		-2.734613	1	1	120908	7	43	1	0	1	1	1.897148	1	0.150000	1.900000	0.090666	0.120000	0.040000	0.240000	0.110000	0.132143	0.120000	0	0.070000	0.180000
KRT80	144501	broad.mit.edu	37	12	52566851	52566851	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr12:52566851G>A	ENST00000394815.2	-	6	1025	c.928C>T	c.(928-930)Cgg>Tgg	p.R310W	KRT80_ENST00000313234.5_Missense_Mutation_p.R310W	NM_182507.2	NP_872313.2	Q6KB66	K2C80_HUMAN	keratin 80			5					ATCTGGGACCGCAGCTTCTGG	0.637000													GBM(178;2309 2916 15678 35873)											0							SO:0001583	missense			ENST00000394815.2	0	1	hg19	CCDS8821.2	2	9.157509157509158E-4	0	0.0	0	0.0	2	0.0034965034965034965	0	0.0	g	14.10	2.434757	0.43224	0.0	1.16E-4	ENSG00000167767	ENST00000313234;ENST00000394815	D;D	0.89270	-2.49;-2.49	4.39	1.24	0.21308	Filament (1);	0.000000	0.34725	N	0.003726	D	0.93726	0.7995	M	0.80422	2.495	0.19300	N	0.999974	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.984;0.991;0.998	D	0.88202	0.2884	10	0.87932	D	0	.	14.4952	0.67683	0.0:0.0:0.5428:0.4572	.	310;310;345	Q6KB66-2;Q6KB66;Q6KB66-3	.;K2C80_HUMAN;.	W	310	ENSP00000369361:R310W;ENSP00000378292:R310W	ENSP00000369361:R310W	R	-	1	2	KRT80	50853118	0.000000	0.05858	0.287000	0.24848	0.492000	0.33523	0.185000	0.16958	0.577000	0.29470	-0.217000	0.12591	CGG		TCGA-IB-A5SQ-01A-11D-A32N-08	KRT80-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000316757.1	0	0	0	6	325	0	55	0	2.880270e-01	0	51	0	55	2		0	0	0	0	0	2	1	0.964007	6	321	0	55	2	0	0	0	0	0	0		-3.694595	1	1	121412	34	45	1	1	2	3	2.044214	0	0.150000	1.900000	0.159456	0.270000	0.110000	1.000000	0.240000	0.364578	0.270000	0	0.170000	0.470000
GPR162	27239	broad.mit.edu	37	12	6933844	6933844	+	Silent	SNP	G	G	A			TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr12:6933844G>A	ENST00000311268.3	+	2	1567	c.780G>A	c.(778-780)tcG>tcA	p.S260S	GPR162_ENST00000382315.3_Intron|GPR162_ENST00000428545.2_Intron	NM_019858.1	NP_062832.1	Q16538	GP162_HUMAN	G protein-coupled receptor 162			18					TGGATGGCTCGGAGTCTGCCA	0.622000																								0							SO:0001819	synonymous_variant			ENST00000311268.3	1	1	hg19	CCDS8563.1																																																																																				TCGA-IB-A5SQ-01A-11D-A32N-08	GPR162-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399478.1	1	0	0	24	348	0	59	0	7.647126e-02	0	7	0	59	2		0	0	0	0	0	2	1	0.749864	24	338	1	57	20	0	0	0	0	0	0		-2.774811	1	1	121410	1	33	1	1	2	3	2.042590	0	0.150000	1.900000	0.159456	0.900000	0.580000	1.000000	1.000000	0.876679	0.900000	1	0.720000	1.000000
CD163	9332	broad.mit.edu	37	12	7635290	7635290	+	Missense_Mutation	SNP	C	C	A	rs139478533	byFrequency	TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08			C	A	C	C		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr12:7635290C>A	ENST00000359156.4	-	14	3398	c.3196G>T	c.(3196-3198)Gtc>Ttc	p.V1066F	CD163_ENST00000541972.1_Missense_Mutation_p.V1054F|CD163_ENST00000396620.3_Missense_Mutation_p.V1099F|CD163_ENST00000539632.1_5'Flank|CD163_ENST00000432237.2_Missense_Mutation_p.V1066F	NM_004244.5	NP_004235.4	Q86VB7	C163A_HUMAN	CD163 molecule	p.V1066I(1)		76				WF10(DB05389)	AATAATGCGACGAAAATGGCC	0.423000																								1	Substitution - Missense(1)						SO:0001583	missense			ENST00000359156.4	1	1	hg19	CCDS8578.1	.	.	.	.	.	.	.	.	.	.	C	9.345	1.064039	0.20067	.	.	ENSG00000177575	ENST00000359156;ENST00000541972;ENST00000396620;ENST00000432237	T;T;T;T	0.01446	4.88;4.91;4.91;4.91	4.32	-0.639	0.11497	.	1.150940	0.06616	N	0.756554	T	0.01592	0.0051	N	0.08118	0	0.09310	N	1	P;P;P	0.37573	0.532;0.6;0.532	B;B;B	0.41860	0.185;0.368;0.185	T	0.51371	-0.8714	10	0.72032	D	0.01	.	7.6763	0.28488	0.0:0.3086:0.0:0.6914	.	1099;1066;1066	C9JHR8;Q86VB7-3;Q86VB7	.;.;C163A_HUMAN	F	1066;1054;1099;1066	ENSP00000352071:V1066F;ENSP00000444071:V1054F;ENSP00000379863:V1099F;ENSP00000403885:V1066F	ENSP00000352071:V1066F	V	-	1	0	CD163	7526557	0.001000	0.12720	0.001000	0.08648	0.001000	0.01503	-0.734000	0.04893	-0.102000	0.12197	-1.193000	0.01689	GTC		TCGA-IB-A5SQ-01A-11D-A32N-08	CD163-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000399396.2	1	0	0	43	484	0	99	0	1	0	313	0	99	2		0	0	0	0	0	2	1	1.000000	44	477	0	99	2	0	0	0	0	0	0		-11.544490	1	1	0	0		1	1	2	3	2.042590	0	0.150000	1.900000	0.159456	0.990000	0.810000	1.000000	1.000000	0.980894	0.990000	1	0.950000	1.000000
DUSP6	1848	broad.mit.edu	37	12	89745479	89745479	+	Nonsense_Mutation	SNP	G	G	T			TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr12:89745479G>T	ENST00000279488.7	-	1	1569	c.338C>A	c.(337-339)tCg>tAg	p.S113*	DUSP6_ENST00000308385.6_Nonsense_Mutation_p.S113*|DUSP6_ENST00000547291.1_5'Flank|DUSP6_ENST00000547140.1_5'Flank	NM_001946.2	NP_001937.2	Q16828	DUS6_HUMAN	dual specificity phosphatase 6			16					CCCGAGCACCGACTCGCCGCC	0.682000													Colon(132;3456 5224)											0							SO:0001587	stop_gained			ENST00000279488.7	0	1	hg19	CCDS9033.1	.	.	.	.	.	.	.	.	.	.	G	46	12.912705	0.99705	.	.	ENSG00000139318	ENST00000279488;ENST00000308385;ENST00000548755	.	.	.	5.09	5.09	0.68999	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	17.6644	0.88200	0.0:0.0:1.0:0.0	.	.	.	.	X	113	.	ENSP00000279488:S113X	S	-	2	0	DUSP6	88269610	1.000000	0.71417	1.000000	0.80357	0.790000	0.44656	9.616000	0.98359	2.646000	0.89796	0.655000	0.94253	TCG		TCGA-IB-A5SQ-01A-11D-A32N-08	DUSP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406534.2	1	0	0	4	76	0	20	1	8.494142e-01	5	63	0	20	2		0	0	0	0	0	2	1	0.889180	4	75	0	20	2	0	0	0	0	0	0		-8.334806	1	1	0	0		1	0	1	1	1.897148	1	0.150000	1.900000	0.090666	0.600000	0.210000	1.000000	1.000000	0.623294	0.600000	0	0.380000	0.870000
ATP12A	479	broad.mit.edu	37	13	25262530	25262530	+	Missense_Mutation	SNP	C	C	A	rs146927457		TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr13:25262530C>A	ENST00000381946.3	+	4	469	c.302C>A	c.(301-303)aCg>aAg	p.T101K	ATP12A_ENST00000218548.6_Missense_Mutation_p.T101K			P54707	AT12A_HUMAN	ATPase, H+/K+ transporting, nongastric, alpha polypeptide			74		Lung SC(185;0.0225)|Breast(139;0.077)			CCCAAGCAGACGCCTGAGATC	0.587000													Pancreas(156;1582 1935 18898 22665 26498)											0							SO:0001583	missense			ENST00000381946.3	1	1	hg19	CCDS31948.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.097218	0.76870	.	.	ENSG00000075673	ENST00000218548;ENST00000381946	T;T	0.77489	-1.1;-1.1	5.06	5.06	0.68205	ATPase, P-type cation-transporter, N-terminal (2);	0.151867	0.45606	D	0.000357	T	0.82226	0.4991	M	0.64404	1.975	0.80722	D	1	D;D	0.55172	0.957;0.97	P;P	0.52758	0.708;0.473	D	0.83710	0.0187	10	0.56958	D	0.05	.	15.9701	0.80008	0.0:1.0:0.0:0.0	.	101;101	P54707-2;P54707	.;AT12A_HUMAN	K	101	ENSP00000218548:T101K;ENSP00000371372:T101K	ENSP00000218548:T101K	T	+	2	0	ATP12A	24160530	1.000000	0.71417	0.801000	0.32222	0.716000	0.41182	5.692000	0.68256	2.624000	0.88883	0.655000	0.94253	ACG		TCGA-IB-A5SQ-01A-11D-A32N-08	ATP12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044199.1	1	0	0	122	1588	0	389		0	0	0	0	389	2		0	0	0	0	0	2	1	1.000000	122	1563	0	387	2	0	0	0	0	0	0		-19.901080	1	1	0	0		1	0	0	0	1.959332	0	0.150000	1.900000	0.122354	0.910000	0.760000	1.000000	1.000000	0.915991	0.910000	1	0.830000	1.000000
TTC9	23508	broad.mit.edu	37	14	71134284	71134284	+	Missense_Mutation	SNP	G	G	T			TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr14:71134284G>T	ENST00000256367.2	+	2	753	c.410G>T	c.(409-411)tGc>tTc	p.C137F		NM_015351.1	NP_056166.1	Q92623	TTC9A_HUMAN	tetratricopeptide repeat domain 9			1					TCCATAGCCTGCCTGCTCCAG	0.512000																								0							SO:0001583	missense			ENST00000256367.2	1	1	hg19	CCDS45132.1	.	.	.	.	.	.	.	.	.	.	G	17.48	3.400773	0.62177	.	.	ENSG00000133985	ENST00000256367	T	0.17691	2.26	5.02	5.02	0.67125	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.068925	0.64402	D	0.000014	T	0.51686	0.1689	M	0.90425	3.115	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.62353	-0.6872	10	0.87932	D	0	-15.8465	18.5279	0.90980	0.0:0.0:1.0:0.0	.	137	Q92623	TTC9A_HUMAN	F	137	ENSP00000256367:C137F	ENSP00000256367:C137F	C	+	2	0	TTC9	70204037	1.000000	0.71417	1.000000	0.80357	0.319000	0.28217	9.243000	0.95416	2.596000	0.87737	0.655000	0.94253	TGC		TCGA-IB-A5SQ-01A-11D-A32N-08	TTC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417024.1	1	0	0	11	193	0	30	1	5.461245e-01	15	17	0	30	2		0	0	0	0	0	2	1	0.998386	11	191	0	30	2	0	0	0	0	0	0		-14.094270	1	1	0	0		1	1	2	3	2.015457	0	0.150000	1.900000	0.153808	0.740000	0.390000	1.000000	1.000000	0.754007	0.740000	0	0.550000	1.000000
FAM181A	90050	broad.mit.edu	37	14	94394668	94394668	+	Missense_Mutation	SNP	T	T	G			TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr14:94394668T>G	ENST00000267594.5	+	3	530	c.223T>G	c.(223-225)Ttc>Gtc	p.F75V	FAM181A_ENST00000557000.2_Missense_Mutation_p.F13V|FAM181A_ENST00000557719.1_Missense_Mutation_p.F13V|FAM181A_ENST00000556222.1_Missense_Mutation_p.F13V|FAM181A-AS1_ENST00000554742.1_RNA	NM_001207073.1|NM_001207074.1|NM_138344.4	NP_001194002.1|NP_001194003.1|NP_612353.3	Q8N9Y4	F181A_HUMAN	family with sequence similarity 181, member A			18					GCTGCTGAACTTCGTGAACCT	0.607000																								0							SO:0001583	missense			ENST00000267594.5	1	1	hg19	CCDS9914.1	.	.	.	.	.	.	.	.	.	.	T	24.6	4.550636	0.86127	.	.	ENSG00000140067	ENST00000557719;ENST00000267594;ENST00000556222;ENST00000554404;ENST00000557000	T;T;T;T	0.72835	-0.69;-0.69;-0.69;-0.69	4.63	4.63	0.57726	.	0.000000	0.64402	D	0.000019	T	0.81559	0.4848	M	0.64404	1.975	0.58432	D	0.999994	D	0.89917	1.0	D	0.87578	0.998	D	0.83842	0.0258	10	0.87932	D	0	-15.2697	14.0621	0.64806	0.0:0.0:0.0:1.0	.	75	Q8N9Y4	F181A_HUMAN	V	13;75;13;13;64	ENSP00000451802:F13V;ENSP00000267594:F75V;ENSP00000451678:F13V;ENSP00000452393:F13V	ENSP00000267594:F75V	F	+	1	0	FAM181A	93464421	1.000000	0.71417	0.998000	0.56505	0.972000	0.66771	8.018000	0.88722	1.733000	0.51620	0.260000	0.18958	TTC		TCGA-IB-A5SQ-01A-11D-A32N-08	FAM181A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000412840.1	1	0	0	16	330	0	70		0	0	0	0	70	2		0	0	0	0	0	2	1	0.999932	16	326	0	70	2	0	0	0	0	0	0		-17.751810	1	1	0	0		1	1	2	3	2.015457	0	0.150000	1.900000	0.153808	0.630000	0.370000	1.000000	0.610000	0.659359	0.630000	0	0.490000	0.830000
RYR3	6263	broad.mit.edu	37	15	33795853	33795853	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr15:33795853G>A	ENST00000389232.4	+	3	263	c.193G>A	c.(193-195)Gtc>Atc	p.V65I	RYR3_ENST00000415757.3_Missense_Mutation_p.V65I	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3			311		all_lung(180;7.18e-09)			AGATCTCTGCGTCTGCAATTT	0.473000																								0							SO:0001583	missense			ENST00000389232.4	0	1	hg19	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	G	8.783	0.928601	0.18131	.	.	ENSG00000198838	ENST00000389232;ENST00000415757;ENST00000361728	D;D	0.98164	-4.76;-4.76	5.36	3.36	0.38483	Inositol 1,4,5-trisphosphate/ryanodine receptor (1);	0.069726	0.56097	D	0.000033	D	0.87811	0.6271	N	0.00436	-1.5	0.32828	D	0.503591	B;B	0.09022	0.002;0.001	B;B	0.06405	0.002;0.001	D	0.85323	0.1085	10	0.22706	T	0.39	.	5.095	0.14729	0.3515:0.0:0.6485:0.0	.	65;65	Q15413-2;Q15413	.;RYR3_HUMAN	I	65	ENSP00000373884:V65I;ENSP00000399610:V65I	ENSP00000354735:V65I	V	+	1	0	RYR3	31583145	0.998000	0.40836	0.994000	0.49952	0.995000	0.86356	2.728000	0.47319	1.479000	0.48272	0.655000	0.94253	GTC		TCGA-IB-A5SQ-01A-11D-A32N-08	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1	0	0	0	5	96	0	16		0	0	0	0	16	2		0	0	0	0	0	2	1	0.939157	5	96	0	16	2	0	0	0	0	0	0		-4.379368	1	1	120856	31	42	1	0	1	1	2.007251	0	0.150000	1.900000	0.144869	0.680000	0.260000	1.000000	1.000000	0.694824	0.680000	0	0.440000	0.990000
SPRED1	161742	broad.mit.edu	37	15	38643373	38643373	+	Missense_Mutation	SNP	G	G	C			TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr15:38643373G>C	ENST00000299084.4	+	7	1703	c.843G>C	c.(841-843)caG>caC	p.Q281H		NM_152594.2	NP_689807.1	Q7Z699	SPRE1_HUMAN	sprouty-related, EVH1 domain containing 1			25		all_cancers(109;4.88e-13)|all_epithelial(112;1.83e-11)|Lung NSC(122;2.21e-09)|all_lung(180;4.64e-08)|Melanoma(134;0.091)			CCAGTATTCAGTTTTCTAAAC	0.398000									Legius syndrome				Melanoma(196;2146 2959 7698 16532)											0							SO:0001583	missense	Familial Cancer Database	Neurofibromatosis type 1 - like syndrome, SPRED1 disorder	ENST00000299084.4	1	1	hg19	CCDS32193.1	.	.	.	.	.	.	.	.	.	.	G	0.672	-0.801388	0.02841	.	.	ENSG00000166068	ENST00000299084	D	0.84298	-1.83	5.97	-0.439	0.12264	c-Kit-binding domain (1);	0.734032	0.14484	N	0.316776	T	0.69205	0.3085	N	0.14661	0.345	0.21325	N	0.999728	B	0.02656	0.0	B	0.01281	0.0	T	0.52358	-0.8586	10	0.24483	T	0.36	-18.8552	9.1329	0.36857	0.2898:0.2295:0.4807:0.0	.	281	Q7Z699	SPRE1_HUMAN	H	281	ENSP00000299084:Q281H	ENSP00000299084:Q281H	Q	+	3	2	SPRED1	36430665	0.847000	0.29606	0.971000	0.41717	0.969000	0.65631	0.024000	0.13555	-0.315000	0.08703	-0.153000	0.13522	CAG		TCGA-IB-A5SQ-01A-11D-A32N-08	SPRED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418217.1	1	0	1	32	297	0	57	1	9.194709e-01	9	33	0	57	2		0	0	0	0	0	2	1	1.000000	31	294	0	57	2	0	0	0	0	0	0		-11.738120	1	1	0	0		1	0	1	1	2.007251	0	0.150000	1.900000	0.144869	0.990000	0.900000	1.000000	1.000000	0.994310	0.990000	1	0.990000	1.000000
KIAA0430	9665	broad.mit.edu	37	16	15729930	15729930	+	Silent	SNP	C	C	T			TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr16:15729930C>T	ENST00000396368.3	-	3	620	c.414G>A	c.(412-414)tcG>tcA	p.S138S	KIAA0430_ENST00000602337.1_Silent_p.S138S|KIAA0430_ENST00000344181.3_5'UTR|KIAA0430_ENST00000540441.2_Silent_p.S138S|KIAA0430_ENST00000548025.1_Silent_p.S138S|KIAA0430_ENST00000551742.1_Silent_p.S138S	NM_001184998.1|NM_001184999.1|NM_014647.3	NP_001171927.1|NP_001171928.1|NP_055462.2	Q9Y4F3	MARF1_HUMAN	KIAA0430			40					TGGTGCTTTGCGAGTCTAACA	0.547000																								0							SO:0001819	synonymous_variant			ENST00000396368.3	0	1	hg19	CCDS10562.2																																																																																				TCGA-IB-A5SQ-01A-11D-A32N-08	KIAA0430-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252131.2	0	0	0	7	750	1	141	0	2.029803e-02	0	20	1	141	2		0	0	0	0	0	2	0	0.018554	7	737	1	139	18	0	0	0	0	0	0		-1.980703	0	1	121032	16	47	1	1	2	3	2.021185	0	0.150000	1.900000	0.155070	0.130000	0.050000	1.000000	0.130000	0.195668	0.130000	0	0.080000	0.210000
ARHGAP17	55114	broad.mit.edu	37	16	24942323	24942323	+	Missense_Mutation	SNP	A	A	G			TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08			A	G	A	A		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr16:24942323A>G	ENST00000289968.6	-	19	2366	c.2297T>C	c.(2296-2298)cTa>cCa	p.L766P	ARHGAP17_ENST00000441763.2_3'UTR|ARHGAP17_ENST00000303665.5_Missense_Mutation_p.L688P	NM_001006634.1	NP_001006635.1	Q68EM7	RHG17_HUMAN	Rho GTPase activating protein 17			30					CTGTTTTCCTAGGGGCGGAGT	0.617000																								0							SO:0001583	missense			ENST00000289968.6	1	1	hg19	CCDS32409.1	.	.	.	.	.	.	.	.	.	.	A	10.85	1.466931	0.26335	.	.	ENSG00000140750	ENST00000289968;ENST00000303665;ENST00000455311	T;T	0.20738	2.05;2.08	5.39	4.27	0.50696	.	0.234011	0.21868	N	0.067922	T	0.34454	0.0898	L	0.41356	1.27	0.31123	N	0.708582	B;B;D;B;B	0.89917	0.004;0.003;1.0;0.137;0.215	B;B;D;B;B	0.91635	0.011;0.005;0.999;0.066;0.139	T	0.28138	-1.0053	10	0.54805	T	0.06	.	9.6939	0.40145	0.9158:0.0:0.0842:0.0	.	688;766;299;599;327	Q68EM7-2;Q68EM7;Q68EM7-7;B4DWE9;B4DVF3	.;RHG17_HUMAN;.;.;.	P	766;688;766	ENSP00000289968:L766P;ENSP00000303130:L688P	ENSP00000289968:L766P	L	-	2	0	ARHGAP17	24849824	0.862000	0.29867	0.018000	0.16275	0.069000	0.16628	3.540000	0.53611	0.829000	0.34733	0.454000	0.30748	CTA		TCGA-IB-A5SQ-01A-11D-A32N-08	ARHGAP17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436548.3	1	0	1	72	710	0	165	1	9.988698e-01	19	80	0	165	2		0	0	0	0	0	2	1	1.000000	71	704	0	163	2	0	0	0	0	0	0		-19.482530	1	1	0	0		1	0	1	1	2.006314	0	0.150000	1.900000	0.144869	0.990000	0.960000	1.000000	1.000000	0.997926	0.990000	1	0.990000	1.000000
ZACN	353174	broad.mit.edu	37	17	74077738	74077738	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr17:74077738G>A	ENST00000334586.5	+	7	865	c.782G>A	c.(781-783)cGc>cAc	p.R261H	EXOC7_ENST00000332065.5_3'UTR|EXOC7_ENST00000589210.1_3'UTR|EXOC7_ENST00000591724.1_Intron|EXOC7_ENST00000607838.1_3'UTR	NM_180990.3	NP_851321.2	Q401N2	ZACN_HUMAN	zinc activated ligand-gated ion channel			11					GCCATTGAGCGCATAGGCTAC	0.622000																								0							SO:0001583	missense			ENST00000334586.5	0	1	hg19	CCDS11740.2	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	9.702	1.154853	0.21371	.	.	ENSG00000186919	ENST00000334586	D	0.88431	-2.38	4.64	2.61	0.31194	Neurotransmitter-gated ion-channel transmembrane domain (1);	0.154450	0.43110	N	0.000602	D	0.83755	0.5323	M	0.78285	2.405	0.20196	N	0.999922	P	0.42518	0.782	B	0.28232	0.087	T	0.77517	-0.2558	10	0.87932	D	0	-15.7124	6.8633	0.24079	0.0924:0.0:0.7344:0.1732	.	261	Q401N2	ZACN_HUMAN	H	261	ENSP00000334854:R261H	ENSP00000334854:R261H	R	+	2	0	ZACN	71589333	0.751000	0.28327	0.017000	0.16124	0.217000	0.24651	1.805000	0.38883	0.557000	0.29117	0.505000	0.49811	CGC		TCGA-IB-A5SQ-01A-11D-A32N-08	ZACN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347827.2	0	0	0	6	688	0	136	0	5.713662e-01	0	203	0	136	2		0	0	0	0	0	2	1	0.963140	4	678	0	134	2	0	0	0	0	0	0		-1.756895	0	1	121412	1	33	1	0	1	1	2.012279	0	0.150000	1.900000	0.146158	0.120000	0.040000	0.240000	0.120000	0.132377	0.120000	0	0.070000	0.180000
SMARCA4	6597	broad.mit.edu	37	19	11143994	11143994	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr19:11143994G>A	ENST00000429416.3	+	27	3856	c.3575G>A	c.(3574-3576)cGc>cAc	p.R1192H	SMARCA4_ENST00000590574.1_Missense_Mutation_p.R1192H|SMARCA4_ENST00000541122.2_Missense_Mutation_p.R1192H|SMARCA4_ENST00000413806.3_Missense_Mutation_p.R1192H|SMARCA4_ENST00000450717.3_Missense_Mutation_p.R1192H|SMARCA4_ENST00000444061.3_Missense_Mutation_p.R1192H|SMARCA4_ENST00000344626.4_Missense_Mutation_p.R1192H|SMARCA4_ENST00000358026.2_Missense_Mutation_p.R1192H|SMARCA4_ENST00000589677.1_Missense_Mutation_p.R1192H	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	p.?(1)		163		all_lung(6;0.0512)|Lung NSC(9;0.0568)			CGAGCCCACCGCATCGGGCAG	0.612000			F, N, Mis		NSCLC										Rec	yes		19	19p13.2	6597	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4		E	1	Unknown(1)						SO:0001583	missense			ENST00000429416.3	1	1	hg19	CCDS12253.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.769759	0.90020	.	.	ENSG00000127616	ENST00000429416;ENST00000358026;ENST00000421844;ENST00000344626;ENST00000541122;ENST00000444061;ENST00000450717;ENST00000413806	D;D;D;D;D;D;D	0.97850	-4.57;-4.57;-4.57;-4.57;-4.57;-4.57;-4.57	4.74	4.74	0.60224	Helicase, C-terminal (3);	0.000000	0.85682	D	0.000000	D	0.99426	0.9797	H	0.99863	4.86	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D	0.97804	1.0246	10	0.87932	D	0	-34.1151	16.7067	0.85374	0.0:0.0:1.0:0.0	.	1192;1192;1192;1192;1192;412;1192	B1A8Z6;B1A8Z4;B1A8Z7;Q9HBD4;B1A8Z5;B4E0F1;P51532	.;.;.;.;.;.;SMCA4_HUMAN	H	1192;1192;1256;1192;1192;1192;1192;1192	ENSP00000395654:R1192H;ENSP00000350720:R1192H;ENSP00000343896:R1192H;ENSP00000445036:R1192H;ENSP00000392837:R1192H;ENSP00000397783:R1192H;ENSP00000414727:R1192H	ENSP00000343896:R1192H	R	+	2	0	SMARCA4	11004994	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	9.319000	0.96338	2.488000	0.83962	0.558000	0.71614	CGC		TCGA-IB-A5SQ-01A-11D-A32N-08	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	1	0	1	18	374	0	73	1	9.647176e-01	16	100	0	73	2	1	9.999961e-01	55	895	1	573	8	1	0.999980	18	366	0	73	2	0	0	0	0	0	0		-4.595885	1	1	0	0		1	0	1	1	2.007438	0	0.150000	1.900000	0.144869	0.610000	0.370000	0.910000	0.590000	0.628884	0.610000	0	0.480000	0.760000
PKN1	5585	broad.mit.edu	37	19	14581660	14581660	+	Silent	SNP	C	C	T			TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr19:14581660C>T	ENST00000242783.6	+	21	2787	c.2622C>T	c.(2620-2622)ttC>ttT	p.F874F	PKN1_ENST00000342216.4_Silent_p.F880F	NM_002741.3	NP_002732.3	Q16512	PKN1_HUMAN	protein kinase N1			31					AGCCCTTCTTCAGGGTGAGAT	0.607000													NSCLC(185;2539 2965 10733 52867)											0							SO:0001819	synonymous_variant			ENST00000242783.6	1	1	hg19	CCDS42513.1																																																																																				TCGA-IB-A5SQ-01A-11D-A32N-08	PKN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095510.1	1	0	0	26	344	0	57	1	9.999999e-01	41	318	0	57	2		0	0	0	0	0	2	1	1.000000	26	336	0	57	2	0	0	0	0	0	0		-3.318806	1	1	0	0		1	0	1	1	2.007438	0	0.150000	1.900000	0.144869	0.920000	0.620000	1.000000	1.000000	0.899389	0.920000	1	0.760000	1.000000
SHD	56961	broad.mit.edu	37	19	4283173	4283173	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr19:4283173C>T	ENST00000543264.2	+	3	1989	c.526C>T	c.(526-528)Cgg>Tgg	p.R176W	SHD_ENST00000599689.1_Missense_Mutation_p.R176W	NM_020209.3	NP_064594.3	Q96IW2	SHD_HUMAN	Src homology 2 domain containing transforming protein D			14					GGAAGATGAACGGCCAGCAGA	0.567000																								0							SO:0001583	missense			ENST00000543264.2	1	1	hg19	CCDS12125.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	21.6	4.175397	0.78564	.	.	ENSG00000105251	ENST00000543264;ENST00000221852	T	0.35973	1.28	5.47	3.27	0.37495	.	0.000000	0.85682	D	0.000000	T	0.59362	0.2188	M	0.80332	2.49	0.42300	D	0.992177	D	0.89917	1.0	D	0.76071	0.987	T	0.63346	-0.6658	10	0.87932	D	0	-10.4695	11.5411	0.50667	0.4875:0.5125:0.0:0.0	.	176	Q96IW2	SHD_HUMAN	W	176;91	ENSP00000446058:R176W	ENSP00000221852:R91W	R	+	1	2	SHD	4234173	0.997000	0.39634	0.968000	0.41197	0.970000	0.65996	0.914000	0.28624	0.607000	0.29982	0.448000	0.29417	CGG		TCGA-IB-A5SQ-01A-11D-A32N-08	SHD-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458082.1	1	0	0	21	315	0	48		0	0	0	0	48	2		0	0	0	0	0	2	1	0.999998	21	311	0	48	2	0	0	0	0	0	0		-3.222166	1	1	121412	6	40	1	0	1	1	2.007438	0	0.150000	1.900000	0.144869	0.820000	0.530000	1.000000	1.000000	0.826884	0.820000	0	0.660000	1.000000
GIPR	2696	broad.mit.edu	37	19	46178073	46178073	+	Missense_Mutation	SNP	C	C	G			TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr19:46178073C>G	ENST00000590918.1	+	7	721	c.622C>G	c.(622-624)Ctg>Gtg	p.L208V	GIPR_ENST00000304207.8_Missense_Mutation_p.L172V|MIR642A_ENST00000385039.1_RNA|GIPR_ENST00000263281.3_Missense_Mutation_p.L208V	NM_000164.2	NP_000155.1	P48546	GIPR_HUMAN	gastric inhibitory polypeptide receptor			12		Ovarian(192;0.051)|all_neural(266;0.112)			GGCCCTTGCGCTGTGGAACCA	0.577000																								0							SO:0001583	missense			ENST00000590918.1	0	1	hg19	CCDS12671.1	.	.	.	.	.	.	.	.	.	.	C	0.067	-1.209882	0.01555	.	.	ENSG00000010310	ENST00000263281;ENST00000304207	T;T	0.57907	0.37;1.21	4.29	2.14	0.27477	GPCR, family 2-like (1);	0.694941	0.12035	N	0.505605	T	0.29749	0.0743	N	0.04959	-0.14	0.09310	N	1	B;P;B	0.40000	0.187;0.698;0.17	B;B;B	0.40825	0.145;0.341;0.2	T	0.09100	-1.0690	10	0.29301	T	0.29	.	6.6579	0.22998	0.0:0.7816:0.0:0.2184	.	172;208;208	B7WP14;P48546;P48546-2	.;GIPR_HUMAN;.	V	208;172	ENSP00000263281:L208V;ENSP00000305321:L172V	ENSP00000263281:L208V	L	+	1	2	GIPR	50869913	0.163000	0.22920	0.137000	0.22149	0.030000	0.12068	0.778000	0.26732	0.565000	0.29255	-0.258000	0.10820	CTG		TCGA-IB-A5SQ-01A-11D-A32N-08	GIPR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000459640.1	0	0	0	4	250	0	44	0	8.748650e-03	0	7	0	44	2		0	0	0	0	0	2	0	0.883417	0	246	0	44	2	0	0	0	0	0	0		-5.778242	1	0	0	0		1	0	1	1	2.008035	0	0.150000	1.900000	0.144869	0.230000	0.070000	0.490000	0.210000	0.252861	0.230000	0	0.130000	0.360000
KLK11	11012	broad.mit.edu	37	19	51527499	51527499	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr19:51527499C>T	ENST00000594768.1	-	4	546	c.361G>A	c.(361-363)Gcc>Acc	p.A121T	KLK11_ENST00000600362.1_Intron|KLK11_ENST00000319720.7_Missense_Mutation_p.A89T|KLK11_ENST00000594458.1_5'UTR|KLK11_ENST00000453757.3_Missense_Mutation_p.A89T|KLK11_ENST00000391804.3_Missense_Mutation_p.A114T	NM_144947.1	NP_659196.1	Q9UBX7	KLK11_HUMAN	kallikrein-related peptidase 11			7		all_neural(266;0.026)			GACTCAGTGGCTGTCCGGGTC	0.582000																								0							SO:0001583	missense			ENST00000594768.1	1	1	hg19	CCDS12818.1	.	.	.	.	.	.	.	.	.	.	c	13.83	2.354005	0.41700	.	.	ENSG00000167757	ENST00000391804;ENST00000319720;ENST00000453757;ENST00000319756	D;D;D	0.92965	-3.14;-3.14;-3.14	4.32	3.25	0.37280	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.37906	U	0.001893	D	0.86531	0.5955	L	0.37897	1.145	0.30572	N	0.763413	B;B	0.29341	0.242;0.242	B;B	0.32393	0.145;0.145	D	0.83710	0.0187	10	0.72032	D	0.01	.	7.0907	0.25282	0.1979:0.6103:0.1918:0.0	.	121;114	Q9UBX7;Q8IXD7	KLK11_HUMAN;.	T	114;89;89;121	ENSP00000375680:A114T;ENSP00000324269:A89T;ENSP00000413958:A89T	ENSP00000324269:A89T	A	-	1	0	KLK11	56219311	0.152000	0.22762	0.709000	0.30452	0.782000	0.44232	0.785000	0.26830	0.977000	0.38444	0.462000	0.41574	GCC		TCGA-IB-A5SQ-01A-11D-A32N-08	KLK11-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000464314.2	1	0	1	24	518	0	108	1	8.559714e-01	40	37	0	108	2		0	0	0	0	0	2	1	1.000000	24	509	0	104	2	0	0	0	0	0	0		-4.825924	1	1	0	0		1	0	1	1	2.008035	0	0.150000	1.900000	0.144869	0.580000	0.380000	0.830000	0.590000	0.602366	0.580000	0	0.480000	0.710000
DCST1	149095	broad.mit.edu	37	1	155014235	155014235	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr1:155014235G>A	ENST00000295542.1	+	8	890	c.794G>A	c.(793-795)cGc>cAc	p.R265H	DCST1_ENST00000392480.1_Missense_Mutation_p.R265H|DCST1_ENST00000368419.2_Missense_Mutation_p.R265H|DCST1_ENST00000423025.2_Missense_Mutation_p.R240H	NM_152494.3	NP_689707.2	Q5T197	DCST1_HUMAN	DC-STAMP domain containing 1			27	all_epithelial(22;1.43e-30)|all_lung(78;6.64e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.000434)		TGGTTTGACCGCAAGCATGAA	0.537000																								0							SO:0001583	missense			ENST00000295542.1	0	1	hg19	CCDS1083.1	.	.	.	.	.	.	.	.	.	.	G	12.43	1.935876	0.34189	.	.	ENSG00000163357	ENST00000295542;ENST00000392480;ENST00000423025;ENST00000368419	T;T;T;T	0.59224	0.28;0.28;0.28;0.28	4.73	-6.0	0.02206	.	2.011450	0.02298	N	0.070951	T	0.11024	0.0269	N	0.00926	-1.1	0.09310	N	1	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.13872	-1.0493	10	0.41790	T	0.15	0.7543	13.3586	0.60642	0.386:0.0:0.614:0.0	.	240;290;265	E9PHV3;E9PJX3;Q5T197	.;.;DCST1_HUMAN	H	265;265;240;265	ENSP00000295542:R265H;ENSP00000376271:R265H;ENSP00000387369:R240H;ENSP00000357404:R265H	ENSP00000295542:R265H	R	+	2	0	DCST1	153280859	0.000000	0.05858	0.001000	0.08648	0.559000	0.35586	-1.570000	0.02140	-1.129000	0.02918	-1.332000	0.01269	CGC		TCGA-IB-A5SQ-01A-11D-A32N-08	DCST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099006.1	0	0	0	7	582	0	90		0	0	0	0	90	2		0	0	0	0	0	2	1	0.980349	7	579	0	90	2	0	0	0	0	0	0		-1.962440	0	1	121412	1	37	1	1	3	4	2.281435	1	0.150000	1.900000	0.252090	0.190000	0.080000	1.000000	0.190000	0.261969	0.190000	0	0.130000	0.300000
LAMB3	3914	broad.mit.edu	37	1	209800758	209800758	+	Silent	SNP	C	C	T			TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr1:209800758C>T	ENST00000356082.4	-	12	1589	c.1455G>A	c.(1453-1455)ccG>ccA	p.P485P	LAMB3_ENST00000391911.1_Silent_p.P485P|LAMB3_ENST00000367030.3_Silent_p.P485P	NM_000228.2	NP_000219.2	Q13751	LAMB3_HUMAN	laminin, beta 3			45					GGGAGTTGTGCGGGTCGCAGG	0.647000											OREG0014217	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)												0							SO:0001819	synonymous_variant			ENST00000356082.4	0	1	hg19	CCDS1487.1																																																																																				TCGA-IB-A5SQ-01A-11D-A32N-08	LAMB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088525.2	0	0	0	5	248	0	44	0	9.668803e-01	0	316	0	44	2		0	0	0	0	0	2	1	0.938151	5	248	0	44	2	0	0	0	0	0	0		-2.532101	1	1	0	0		1	0	1	1	2.008661	0	0.150000	1.900000	0.144869	0.280000	0.100000	0.560000	0.260000	0.304593	0.280000	0	0.170000	0.420000
WNT3A	89780	broad.mit.edu	37	1	228210456	228210456	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr1:228210456C>T	ENST00000284523.1	+	2	238	c.160C>T	c.(160-162)Cgc>Tgc	p.R54C	WNT3A_ENST00000366753.2_Missense_Mutation_p.R54C	NM_033131.3	NP_149122.1	P56704	WNT3A_HUMAN	wingless-type MMTV integration site family, member 3A			12		Prostate(94;0.0405)			CAAGCAGCTCCGCTTCTGCAG	0.652000																								0							SO:0001583	missense			ENST00000284523.1	1	1	hg19	CCDS1564.1	.	.	.	.	.	.	.	.	.	.	C	27.1	4.803864	0.90623	.	.	ENSG00000154342	ENST00000284523;ENST00000366753	T;T	0.77489	-1.1;-1.1	4.47	4.47	0.54385	.	0.068061	0.64402	D	0.000010	D	0.90573	0.7045	M	0.92970	3.365	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.99	D	0.93130	0.6532	10	0.87932	D	0	.	16.9039	0.86120	0.0:1.0:0.0:0.0	.	54;54	P56704;Q3SY79	WNT3A_HUMAN;.	C	54	ENSP00000284523:R54C;ENSP00000355715:R54C	ENSP00000284523:R54C	R	+	1	0	WNT3A	226277079	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.534000	0.82004	2.311000	0.77944	0.586000	0.80456	CGC		TCGA-IB-A5SQ-01A-11D-A32N-08	WNT3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091648.1	1	0	0	29	281	0	63		0	0	0	0	63	2		0	0	0	0	0	2	1	1.000000	29	275	0	63	2	0	0	0	0	0	0		-3.017764	1	1	0	0		1	0	1	1	2.008661	0	0.150000	1.900000	0.144869	0.990000	0.850000	1.000000	1.000000	0.989552	0.990000	1	0.990000	1.000000
MACF1	23499	broad.mit.edu	37	1	39833893	39833893	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr1:39833893C>T	ENST00000372915.3	+	49	12947	c.12860C>T	c.(12859-12861)tCt>tTt	p.S4287F	MACF1_ENST00000564288.1_Missense_Mutation_p.S4282F|MACF1_ENST00000289893.4_Missense_Mutation_p.S2722F|MACF1_ENST00000476350.1_3'UTR|MACF1_ENST00000361689.2_Missense_Mutation_p.S2220F|MACF1_ENST00000539005.1_Missense_Mutation_p.S2220F|MACF1_ENST00000567887.1_Missense_Mutation_p.S4319F|MACF1_ENST00000317713.7_Missense_Mutation_p.S2220F|MACF1_ENST00000545844.1_Missense_Mutation_p.S2220F			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1			203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)		GAACTGAGCTCTTGTGGCTTT	0.448000																								0							SO:0001583	missense			ENST00000372915.3	1	1	hg19		.	.	.	.	.	.	.	.	.	.	C	22.8	4.340087	0.81911	.	.	ENSG00000127603	ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000289893	T;T;T;T;T;T	0.65178	-0.11;1.23;-0.11;-0.14;0.03;1.0	5.85	3.83	0.44106	.	0.499782	0.18532	N	0.138463	T	0.72993	0.3530	L	0.53249	1.67	0.80722	D	1	D;B;P;B	0.76494	0.999;0.089;0.942;0.033	D;B;P;B	0.72982	0.979;0.052;0.708;0.03	T	0.73418	-0.3989	10	0.52906	T	0.07	.	12.4341	0.55590	0.1331:0.7388:0.1281:0.0	.	4287;2220;2220;2185	Q9UPN3;F8W8Q1;Q9UPN3-2;Q9UPN3-3	MACF1_HUMAN;.;.;.	F	2220;4287;2220;2220;2220;2722	ENSP00000439537:S2220F;ENSP00000362006:S4287F;ENSP00000354573:S2220F;ENSP00000313438:S2220F;ENSP00000444364:S2220F;ENSP00000289893:S2722F	ENSP00000289893:S2722F	S	+	2	0	MACF1	39606480	0.979000	0.34478	0.995000	0.50966	0.977000	0.68977	1.987000	0.40687	1.418000	0.47098	0.467000	0.42956	TCT		TCGA-IB-A5SQ-01A-11D-A32N-08	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	1	0	0	25	345	0	72	0	1.048907e-01	1	7	0	72	2	1	1	35	594	0	385	2	1	1.000000	25	342	0	70	2	0	0	0	0	0	0		-3.017775	1	1	0	0		1	2	2	4	2.125106	1	0.150000	1.900000	0.196977	0.990000	0.650000	1.000000	1.000000	0.933194	0.990000	1	0.810000	1.000000
YTHDF1	54915	broad.mit.edu	37	20	61834082	61834082	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr20:61834082G>A	ENST00000370339.3	-	4	1551	c.1210C>T	c.(1210-1212)Cgc>Tgc	p.R404C	YTHDF1_ENST00000370334.4_Intron|YTHDF1_ENST00000370333.4_Missense_Mutation_p.R354C	NM_017798.3	NP_060268.2	Q9BYJ9	YTHD1_HUMAN	YTH domain family, member 1			24					TTAATGGAGCGGTGGATGTCG	0.552000																								0							SO:0001583	missense			ENST00000370339.3	1	1	hg19	CCDS13511.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.105768	0.77096	.	.	ENSG00000149658	ENST00000370339;ENST00000370333	T;T	0.31769	1.48;1.48	4.72	4.72	0.59763	YTH domain (2);	0.047653	0.85682	N	0.000000	T	0.64438	0.2598	M	0.90082	3.085	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.74179	-0.3749	10	0.87932	D	0	-12.6731	18.0486	0.89341	0.0:0.0:1.0:0.0	.	404	Q9BYJ9	YTHD1_HUMAN	C	404;354	ENSP00000359364:R404C;ENSP00000359358:R354C	ENSP00000359358:R354C	R	-	1	0	YTHDF1	61304527	1.000000	0.71417	0.999000	0.59377	0.762000	0.43233	9.669000	0.98622	2.339000	0.79563	0.591000	0.81541	CGC		TCGA-IB-A5SQ-01A-11D-A32N-08	YTHDF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080110.2	1	0	1	36	518	0	93	1	9.526933e-01	19	55	0	93	2		0	0	0	0	0	2	1	1.000000	37	507	0	92	2	0	0	0	0	0	0		-2.540643	1	1	0	0		1	0	1	1	2.006475	0	0.150000	1.900000	0.144869	0.850000	0.610000	1.000000	1.000000	0.857691	0.850000	1	0.720000	1.000000
SLC5A3	6526	broad.mit.edu	37	21	35468701	35468701	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr21:35468701G>A	ENST00000381151.3	+	2	1716	c.1204G>A	c.(1204-1206)Gca>Aca	p.A402T	MRPS6_ENST00000399312.2_Intron|AP000320.7_ENST00000362077.4_RNA|SLC5A3_ENST00000608209.1_Missense_Mutation_p.A402T			P53794	SC5A3_HUMAN	solute carrier family 5 (sodium/myo-inositol cotransporter), member 3			20					CCGCAAGAGCGCAAGCTCCCG	0.478000																								0							SO:0001583	missense			ENST00000381151.3	0	1	hg19	CCDS33549.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.122917	0.77436	.	.	ENSG00000198743	ENST00000381151	D	0.89196	-2.48	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	D	0.94301	0.8169	M	0.74881	2.28	0.80722	D	1	D	0.89917	1.0	D	0.75020	0.985	D	0.94516	0.7723	10	0.87932	D	0	.	18.5913	0.91214	0.0:0.0:1.0:0.0	.	402	P53794	SC5A3_HUMAN	T	402	ENSP00000370543:A402T	ENSP00000370543:A402T	A	+	1	0	SLC5A3	34390571	1.000000	0.71417	0.584000	0.28653	0.979000	0.70002	7.792000	0.85828	2.677000	0.91161	0.655000	0.94253	GCA		TCGA-IB-A5SQ-01A-11D-A32N-08	SLC5A3-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000141037.1	0	0	0	5	364	0	48	0	2.021933e-02	0	13	0	48	2		0	0	0	0	0	2	1	0.936150	5	360	0	47	2	0	0	0	0	0	0		-2.648972	1	1	0	0		1	0	1	1	2.014866	0	0.150000	1.900000	0.146158	0.190000	0.070000	0.390000	0.180000	0.211274	0.190000	0	0.120000	0.290000
MKL1	57591	broad.mit.edu	37	22	40807886	40807886	+	Silent	SNP	C	C	T			TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr22:40807886C>T	ENST00000355630.3	-	15	2894	c.2304G>A	c.(2302-2304)ccG>ccA	p.P768P	MKL1_ENST00000407029.1_Silent_p.P768P|MKL1_ENST00000396617.3_Missense_Mutation_p.A772T|MKL1_ENST00000402042.1_Silent_p.P718P	NM_020831.3	NP_065882.1	Q969V6	MKL1_HUMAN	megakaryoblastic leukemia (translocation) 1			30					GCAGGGATGGCGGCTCCTTGA	0.532000			T	RBM15	acute megakaryocytic leukemia										Dom	yes		22	22q13	57591	megakaryoblastic leukemia (translocation) 1		L	0							SO:0001819	synonymous_variant			ENST00000355630.3	0	1	hg19	CCDS14003.1	.	.	.	.	.	.	.	.	.	.	C	13.43	2.235131	0.39498	.	.	ENSG00000196588	ENST00000396617	T	0.46451	0.87	4.92	-7.52	0.01341	.	.	.	.	.	T	0.21022	0.0506	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.29912	-0.9996	8	0.54805	T	0.06	-2.7668	1.9139	0.03293	0.1882:0.3859:0.1944:0.2315	.	772	E7ER32	.	T	772	ENSP00000379861:A772T	ENSP00000379861:A772T	A	-	1	0	MKL1	39137832	0.000000	0.05858	0.090000	0.20809	0.761000	0.43186	-0.214000	0.09292	-0.755000	0.04709	-1.744000	0.00683	GCC		TCGA-IB-A5SQ-01A-11D-A32N-08	MKL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321522.1	0	0	0	7	991	0	151	0	1.857196e-01	0	97	0	151	2		0	0	0	0	0	2	1	0.979377	7	974	0	150	2	0	0	0	0	0	0		-1.952097	0	1	119246	30	48	1	1	2	3	2.016816	1	0.150000	1.900000	0.209302	0.100000	0.030000	0.200000	0.090000	0.114246	0.100000	0	0.060000	0.150000
TTLL1	25809	broad.mit.edu	37	22	43459909	43459909	+	Silent	SNP	G	G	A			TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr22:43459909G>A	ENST00000266254.7	-	7	897	c.657C>T	c.(655-657)tgC>tgT	p.C219C	TTLL1_ENST00000331018.7_Silent_p.C219C	NM_012263.4	NP_036395.1	O95922	TTLL1_HUMAN	tubulin tyrosine ligase-like family, member 1			23		Ovarian(80;0.0694)			TGCAGAACCGGCAAAACCCAA	0.458000																								0							SO:0001819	synonymous_variant			ENST00000266254.7	0	1	hg19	CCDS14043.1	.	.	.	.	.	.	.	.	.	.	G	9.861	1.196399	0.22037	.	.	ENSG00000100271	ENST00000495814	.	.	.	5.98	1.04	0.20106	.	.	.	.	.	T	0.50752	0.1634	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.38023	-0.9680	4	.	.	.	.	4.5385	0.12045	0.3534:0.0:0.4944:0.1523	.	.	.	.	V	145	.	.	A	-	2	0	TTLL1	41789853	1.000000	0.71417	0.986000	0.45419	0.992000	0.81027	2.311000	0.43717	0.359000	0.24239	0.591000	0.81541	GCC		TCGA-IB-A5SQ-01A-11D-A32N-08	TTLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319659.1	0	0	0	6	585	0	104	0	5.549977e-02	0	31	0	104	2		0	0	0	0	0	2	1	0.963229	6	575	0	103	2	0	0	0	0	0	0		-1.866508	0	1	121412	1	32	1	1	2	3	2.016816	1	0.150000	1.900000	0.209302	0.150000	0.050000	0.300000	0.150000	0.168113	0.150000	0	0.100000	0.230000
GLI2	2736	broad.mit.edu	37	2	121736059	121736059	+	Missense_Mutation	SNP	G	G	A	rs150170739		TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr2:121736059G>A	ENST00000452319.1	+	10	1478	c.1418G>A	c.(1417-1419)cGc>cAc	p.R473H	GLI2_ENST00000361492.4_Missense_Mutation_p.R473H|GLI2_ENST00000435313.2_3'UTR|GLI2_ENST00000314490.11_Missense_Mutation_p.R145H					GLI family zinc finger 2			64	Renal(3;0.0496)	Prostate(154;0.0623)			TTTGTGTGCCGCTGGCAGGCC	0.632000																								0							SO:0001583	missense			ENST00000452319.1	0	1	hg19	CCDS33283.1	.	.	.	.	.	.	.	.	.	.	G	16.84	3.234684	0.58886	2.27E-4	1.16E-4	ENSG00000074047	ENST00000452319;ENST00000361492;ENST00000314490	D;D;D	0.91792	-2.91;-2.91;-2.91	4.03	4.03	0.46877	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.115971	0.64402	D	0.000011	D	0.92463	0.7607	N	0.25890	0.77	0.80722	D	1	B;D;D;B;B	0.89917	0.188;1.0;0.983;0.301;0.054	B;D;P;B;B	0.80764	0.035;0.994;0.599;0.052;0.04	D	0.91007	0.4847	10	0.26408	T	0.33	.	16.6998	0.85346	0.0:0.0:1.0:0.0	.	473;456;128;128;145	P10070;Q0VGA0;P10070-2;P10070-4;P10070-3	GLI2_HUMAN;.;.;.;.	H	473;473;145	ENSP00000390436:R473H;ENSP00000354586:R473H;ENSP00000312694:R145H	ENSP00000312694:R145H	R	+	2	0	GLI2	121452529	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.714000	0.84703	2.249000	0.74217	0.491000	0.48974	CGC		TCGA-IB-A5SQ-01A-11D-A32N-08	GLI2-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332293.3	0	0	0	8	858	0	174	0	6.071157e-03	0	11	0	174	2		0	0	0	0	0	2	1	0.988974	11	848	0	172	2	0	0	0	0	0	0		-1.924937	0	1	121410	10	51	1	0	1	1	2.007248	0	0.150000	1.900000	0.144869	0.120000	0.050000	0.230000	0.120000	0.136482	0.120000	0	0.080000	0.180000
KCTD18	130535	broad.mit.edu	37	2	201354855	201354855	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr2:201354855G>A	ENST00000359878.3	-	7	1759	c.1249C>T	c.(1249-1251)Cgg>Tgg	p.R417W	KCTD18_ENST00000409157.1_Missense_Mutation_p.R417W	NM_152387.2	NP_689600.2	Q6PI47	KCD18_HUMAN	potassium channel tetramerization domain containing 18			15					TTCTCAGTCCGCACTCCCAAG	0.592000																								0							SO:0001583	missense			ENST00000359878.3	0	1	hg19	CCDS2330.1	.	.	.	.	.	.	.	.	.	.	G	9.574	1.121811	0.20877	.	.	ENSG00000155729	ENST00000359878;ENST00000409157	T;T	0.35789	1.29;1.29	5.04	2.02	0.26589	.	1.373990	0.04721	N	0.419262	T	0.17492	0.0420	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.17868	-1.0355	10	0.41790	T	0.15	2.0253	4.1114	0.10060	0.2142:0.1959:0.5899:0.0	.	417	Q6PI47	KCD18_HUMAN	W	417	ENSP00000352941:R417W;ENSP00000386751:R417W	ENSP00000352941:R417W	R	-	1	2	KCTD18	201063100	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-0.283000	0.08433	0.715000	0.32103	0.650000	0.86243	CGG		TCGA-IB-A5SQ-01A-11D-A32N-08	KCTD18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256188.1	0	0	0	4	216	0	44	0	2.068375e-01	0	37	0	44	2		0	0	0	0	0	2	1	0.889012	4	214	0	44	2	0	0	0	0	0	0		-3.481862	1	1	0	0		1	0	1	1	2.007248	0	0.150000	1.900000	0.144869	0.260000	0.080000	0.560000	0.240000	0.290519	0.260000	0	0.160000	0.410000
GLB1L	79411	broad.mit.edu	37	2	220104663	220104663	+	Missense_Mutation	SNP	T	T	G			TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr2:220104663T>G	ENST00000295759.7	-	7	1013	c.700A>C	c.(700-702)Acc>Ccc	p.T234P	GLB1L_ENST00000356283.3_Intron|GLB1L_ENST00000409640.1_Intron|GLB1L_ENST00000392089.2_Missense_Mutation_p.T234P|GLB1L_ENST00000497855.1_Intron			Q6UWU2	GLB1L_HUMAN	galactosidase, beta 1-like			22		all_lung(227;1.19e-05)|Lung NSC(271;2.76e-05)|Medulloblastoma(418;0.0208)|Esophageal squamous(248;0.0559)			TCTACAGTGGTATAGAGTCCC	0.527000																								0							SO:0001583	missense			ENST00000295759.7	1	1	hg19	CCDS2437.1	.	.	.	.	.	.	.	.	.	.	T	17.11	3.304575	0.60305	.	.	ENSG00000163521	ENST00000295759;ENST00000392089	D;D	0.97924	-4.61;-4.61	5.37	1.38	0.22167	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.331520	0.36034	N	0.002831	D	0.92169	0.7517	N	0.15975	0.35	0.80722	D	1	B	0.23185	0.081	B	0.28991	0.097	D	0.84745	0.0753	10	0.33940	T	0.23	-4.5903	5.7925	0.18369	0.127:0.2293:0.0:0.6437	.	234	Q6UWU2	GLB1L_HUMAN	P	234	ENSP00000295759:T234P;ENSP00000375939:T234P	ENSP00000295759:T234P	T	-	1	0	GLB1L	219812907	0.814000	0.29104	0.987000	0.45799	0.988000	0.76386	1.378000	0.34328	0.461000	0.27071	0.528000	0.53228	ACC		TCGA-IB-A5SQ-01A-11D-A32N-08	GLB1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256822.2	1	0	0	60	814	0	118	0	6.045220e-02	1	5	0	118	2		0	0	0	0	0	2	1	1.000000	58	801	0	117	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	0	1	1	2.007248	0	0.150000	1.900000	0.144869	0.900000	0.700000	1.000000	1.000000	0.900549	0.900000	1	0.790000	1.000000
DOCK10	55619	broad.mit.edu	37	2	225659771	225659771	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr2:225659771C>T	ENST00000258390.7	-	45	5046	c.4979G>A	c.(4978-4980)cGt>cAt	p.R1660H	DOCK10_ENST00000409592.3_Missense_Mutation_p.R1654H	NM_014689.2	NP_055504.2	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	p.R1658H(1)|p.R198H(1)		87		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)			AGTCCTTATACGCTTAGTCAG	0.478000																								2	Substitution - Missense(2)						SO:0001583	missense			ENST00000258390.7	1	1	hg19	CCDS46528.1	.	.	.	.	.	.	.	.	.	.	C	35	5.577896	0.96565	.	.	ENSG00000135905	ENST00000409592;ENST00000258390;ENST00000373702	T;T	0.65178	4.66;-0.14	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	D	0.83603	0.5290	M	0.91090	3.175	0.58432	D	0.999999	D;P;D;D	0.76494	0.972;0.95;0.984;0.999	B;B;P;D	0.64410	0.444;0.439;0.74;0.925	D	0.86564	0.1843	10	0.87932	D	0	.	20.0637	0.97700	0.0:1.0:0.0:0.0	.	1660;514;1654;322	Q96BY6;B4DF07;B3FL70;B4DEY4	DOC10_HUMAN;.;.;.	H	1654;1660;198	ENSP00000386694:R1654H;ENSP00000258390:R1660H	ENSP00000258390:R1660H	R	-	2	0	DOCK10	225368015	1.000000	0.71417	0.985000	0.45067	0.992000	0.81027	7.487000	0.81328	2.751000	0.94390	0.650000	0.86243	CGT		TCGA-IB-A5SQ-01A-11D-A32N-08	DOCK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331246.1	1	0	0	47	557	0	104	0	6.739727e-01	0	29	0	104	2		0	0	0	0	0	2	1	1.000000	46	550	0	103	2	0	0	0	0	0	0		-11.280890	1	1	0	0		1	0	1	1	2.007248	0	0.150000	1.900000	0.144869	0.990000	0.760000	1.000000	1.000000	0.960975	0.990000	1	0.890000	1.000000
SF3B14	0	broad.mit.edu	37	2	24297040	24297040	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr2:24297040G>A	ENST00000233468.4	-	2	268	c.55C>T	c.(55-57)Cgg>Tgg	p.R19W		NM_016047.3	NP_057131.1						4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				TACAATATCCGATTTACTTCA	0.294000																								0							SO:0001583	missense			ENST00000233468.4	0	1	hg19	CCDS1707.1	.	.	.	.	.	.	.	.	.	.	G	19.84	3.901228	0.72754	.	.	ENSG00000115128	ENST00000233468	T	0.36157	1.27	4.32	4.32	0.51571	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (1);	0.000000	0.85682	D	0.000000	T	0.70962	0.3284	H	0.97077	3.935	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.80708	-0.1262	10	0.87932	D	0	-7.637	12.7778	0.57459	0.0:0.0:0.8358:0.1642	.	19	Q9Y3B4	PM14_HUMAN	W	19	ENSP00000233468:R19W	ENSP00000233468:R19W	R	-	1	2	AC008073.5	24150544	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	3.084000	0.50143	2.351000	0.79841	0.467000	0.42956	CGG		TCGA-IB-A5SQ-01A-11D-A32N-08	SF3B14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246826.1	0	0	0	16	140	0	24	1	1	85	339	0	24	2		0	0	0	0	0	2	1	0.999946	16	139	0	23	2	0	0	0	0	0	0		-19.999590	1	1	121400	3	37	1	0	1	1	2.008170	0	0.150000	1.900000	0.144869	0.990000	0.810000	1.000000	1.000000	0.986971	0.990000	1	0.990000	1.000000
ANTXR1	84168	broad.mit.edu	37	2	69409729	69409729	+	Silent	SNP	G	G	A			TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr2:69409729G>A	ENST00000303714.4	+	16	1612	c.1290G>A	c.(1288-1290)ccG>ccA	p.P430P	RNA5SP96_ENST00000516041.1_RNA|RNU6-1216P_ENST00000362590.2_RNA	NM_032208.2	NP_115584.1	Q9H6X2	ANTR1_HUMAN	anthrax toxin receptor 1			29					TCCCTGAGCCGCGAAATCTCA	0.473000									Familial Infantile Hemangioma															0							SO:0001819	synonymous_variant	Familial Cancer Database	Infantile Capillary Hemangioma, HCI, Hereditary Capillary Hemangioma	ENST00000303714.4	0	1	hg19	CCDS1892.1																																																																																				TCGA-IB-A5SQ-01A-11D-A32N-08	ANTXR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251770.2	0	0	0	5	455	1	82	0	3.709449e-03	0	231	1	82	11		0	0	0	0	0	2	0	0.002879	5	454	1	82	19	0	0	0	0	0	0		-2.426824	0	1	121412	1	32	1	0	1	1	2.008170	0	0.150000	1.900000	0.144869	0.150000	0.050000	0.310000	0.140000	0.169916	0.150000	0	0.090000	0.230000
TET3	200424	broad.mit.edu	37	2	74317154	74317154	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr2:74317154G>A	ENST00000409262.3	+	5	2614	c.2614G>A	c.(2614-2616)Gca>Aca	p.A872T		NM_144993.1	NP_659430.1	O43151	TET3_HUMAN	tet methylcytosine dioxygenase 3			34					GTTCCGCCTCGCAGGGGACAA	0.592000																								0							SO:0001583	missense			ENST00000409262.3	1	1	hg19	CCDS46339.1	.	.	.	.	.	.	.	.	.	.	G	7.764	0.705976	0.15172	.	.	ENSG00000187605	ENST00000409262;ENST00000233310	T	0.11821	2.74	5.3	1.27	0.21489	TET cysteine-rich domain (1);	0.536026	0.21571	N	0.072420	T	0.04182	0.0116	N	0.04508	-0.205	0.09310	N	1	B	0.10296	0.003	B	0.09377	0.004	T	0.43163	-0.9408	10	0.06891	T	0.86	.	5.0566	0.14537	0.4494:0.1493:0.4013:0.0	.	872	O43151	TET3_HUMAN	T	872	ENSP00000386869:A872T	ENSP00000233310:A872T	A	+	1	0	TET3	74170662	0.023000	0.18921	0.016000	0.15963	0.975000	0.68041	0.734000	0.26101	0.331000	0.23511	0.655000	0.94253	GCA		TCGA-IB-A5SQ-01A-11D-A32N-08	TET3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328141.4	1	0	0	51	593	0	102	1	7.892983e-02	3	3	0	102	2	0	0	0	1	0	0	2	1	1.000000	51	579	0	99	2	0	0	0	0	0	0		-12.458530	1	1	121016	1	34	1	0	1	1	2.008170	0	0.150000	1.900000	0.144869	0.990000	0.790000	1.000000	1.000000	0.968882	0.990000	1	0.910000	1.000000
MRPS5	64969	broad.mit.edu	37	2	95767442	95767442	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr2:95767442G>A	ENST00000272418.2	-	8	998	c.790C>T	c.(790-792)Cgg>Tgg	p.R264W		NM_031902.3	NP_114108.1	P82675	RT05_HUMAN	mitochondrial ribosomal protein S5			20					GCATCCATCCGATCAGTAGCT	0.338000																								0							SO:0001583	missense			ENST00000272418.2	0	1	hg19	CCDS2010.1	.	.	.	.	.	.	.	.	.	.	G	13.18	2.159629	0.38119	0.0	1.16E-4	ENSG00000144029	ENST00000272418	.	.	.	5.32	4.44	0.53790	Ribosomal protein S5, N-terminal, conserved site (1);Ribosomal protein S5, N-terminal (2);Double-stranded RNA-binding-like (1);	0.000000	0.85682	D	0.000000	T	0.69314	0.3097	M	0.75447	2.3	0.58432	D	0.999997	D	0.67145	0.996	P	0.58970	0.849	T	0.69665	-0.5084	9	0.37606	T	0.19	-20.9735	11.6662	0.51374	0.0:0.0:0.8223:0.1777	.	264	P82675	RT05_HUMAN	W	264	.	ENSP00000272418:R264W	R	-	1	2	MRPS5	95131169	0.970000	0.33590	0.256000	0.24389	0.096000	0.18686	1.357000	0.34090	1.350000	0.45770	0.591000	0.81541	CGG		TCGA-IB-A5SQ-01A-11D-A32N-08	MRPS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252772.1	1	0	0	8	108	0	18	1	9.873774e-01	11	99	0	18	2		0	0	0	0	0	2	1	0.989080	8	105	0	18	2	0	0	0	0	0	0		-3.307364	1	1	121404	5	32	1	0	1	1	2.008170	0	0.150000	1.900000	0.144869	0.920000	0.440000	1.000000	1.000000	0.856846	0.920000	1	0.650000	1.000000
STXBP5L	9515	broad.mit.edu	37	3	121097633	121097633	+	Silent	SNP	C	C	T			TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr3:121097633C>T	ENST00000273666.6	+	22	2590	c.2319C>T	c.(2317-2319)gcC>gcT	p.A773A	STXBP5L_ENST00000497029.1_Intron|STXBP5L_ENST00000492541.1_Silent_p.A773A|STXBP5L_ENST00000471454.1_Silent_p.A749A|STXBP5L_ENST00000472879.1_Silent_p.A749A	NM_014980.2	NP_055795.1	Q9Y2K9	STB5L_HUMAN	syntaxin binding protein 5-like			68					TTTCTAGTGCCGATGTTTCAA	0.473000																								0							SO:0001819	synonymous_variant			ENST00000273666.6	1	1	hg19	CCDS43137.1																																																																																				TCGA-IB-A5SQ-01A-11D-A32N-08	STXBP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355256.3	1	0	0	8	177	0	38		0	0	0	0	38	2		0	0	0	0	0	2	1	0.989143	8	174	0	38	2	0	0	0	0	0	0		-2.950312	1	1	120778	2	36	1	1	2	3	2.020118	0	0.150000	1.900000	0.154439	0.610000	0.280000	1.000000	1.000000	0.641799	0.610000	0	0.420000	0.880000
NUP210	23225	broad.mit.edu	37	3	13377062	13377062	+	Silent	SNP	G	G	A			TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr3:13377062G>A	ENST00000254508.5	-	28	3817	c.3735C>T	c.(3733-3735)ggC>ggT	p.G1245G	NUP210_ENST00000485755.1_5'Flank	NM_024923.2	NP_079199.2	Q8TEM1	PO210_HUMAN	nucleoporin 210kDa			66	all_neural(104;0.187)				CTTTTACCCGGCCGAGCACGT	0.607000																								0							SO:0001819	synonymous_variant			ENST00000254508.5	1	1	hg19	CCDS33704.1																																																																																				TCGA-IB-A5SQ-01A-11D-A32N-08	NUP210-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340085.1	1	0	0	32	295	0	49	1	5.149085e-01	5	12	0	49	2		0	0	0	0	0	2	1	1.000000	32	292	0	48	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	0	1	1	1.911861	0	0.150000	1.900000	0.081081	0.920000	0.730000	1.000000	0.990000	0.915394	0.920000	1	0.830000	0.980000
KCNH8	131096	broad.mit.edu	37	3	19436644	19436644	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr3:19436644C>T	ENST00000328405.2	+	7	1284	c.1018C>T	c.(1018-1020)Cgt>Tgt	p.R340C	KCNH8_ENST00000475063.1_3'UTR|KCNH8_ENST00000537696.1_5'UTR	NM_144633.2	NP_653234.2	Q96L42	KCNH8_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 8	p.R340C(1)		77					GCGTCTTTTGCGTCTGCTGCA	0.488000													NSCLC(124;1625 1765 8018 24930 42026)											1	Substitution - Missense(1)						SO:0001583	missense			ENST00000328405.2	0	1	hg19	CCDS2632.1	.	.	.	.	.	.	.	.	.	.	C	25.8	4.672024	0.88348	.	.	ENSG00000183960	ENST00000328405	D	0.99523	-6.08	5.78	5.78	0.91487	Ion transport (1);	0.000000	0.32416	U	0.006131	D	0.99722	0.9892	H	0.95679	3.705	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	D	0.97601	1.0123	9	.	.	.	.	20.0118	0.97458	0.0:1.0:0.0:0.0	.	340;340	B7Z398;Q96L42	.;KCNH8_HUMAN	C	340	ENSP00000328813:R340C	.	R	+	1	0	KCNH8	19411648	1.000000	0.71417	0.999000	0.59377	0.789000	0.44602	4.787000	0.62432	2.742000	0.94016	0.650000	0.86243	CGT		TCGA-IB-A5SQ-01A-11D-A32N-08	KCNH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252139.2	0	0	0	5	534	0	107	0	0	0	1	0	107	2		0	0	0	0	0	2	1	0.935642	5	527	0	107	2	0	0	0	0	0	0		-1.963016	0	1	0	0		1	0	1	1	1.911861	0	0.150000	1.900000	0.081081	0.120000	0.040000	0.250000	0.110000	0.133906	0.120000	0	0.070000	0.180000
ARHGAP10	79658	broad.mit.edu	37	4	148944528	148944528	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr4:148944528G>A	ENST00000336498.3	+	19	2070	c.1831G>A	c.(1831-1833)Gtg>Atg	p.V611M	ARHGAP10_ENST00000414545.2_Missense_Mutation_p.V260M	NM_024605.3	NP_078881.3	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 10			33	all_hematologic(180;0.151)	Renal(17;0.0166)			CAAGAGGCCCGTGGCCGTCTA	0.502000																								0							SO:0001583	missense			ENST00000336498.3	1	1	hg19	CCDS34075.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.18|15.18	2.755723|2.755723	0.49362|0.49362	.|.	.|.	ENSG00000071205|ENSG00000071205	ENST00000507661|ENST00000336498;ENST00000414545	.|T;T	.|0.11930	.|3.04;2.73	5.72|5.72	3.96|3.96	0.45880|0.45880	.|.	.|0.543718	.|0.18919	.|N	.|0.127533	T|T	0.25754|0.25754	0.0627|0.0627	L|L	0.40543|0.40543	1.245|1.245	0.36518|0.36518	D|D	0.869994|0.869994	.|D;D;D;D	.|0.89917	.|1.0;0.983;0.993;0.987	.|D;P;P;P	.|0.85130	.|0.997;0.507;0.475;0.475	T|T	0.07385|0.07385	-1.0775|-1.0775	5|10	.|0.46703	.|T	.|0.11	.|.	9.5873|9.5873	0.39524|0.39524	0.0749:0.2861:0.639:0.0|0.0749:0.2861:0.639:0.0	.|.	.|44;192;260;611	.|Q9H7G7;Q86T21;E7EUW5;A1A4S6	.|.;.;.;RHG10_HUMAN	H|M	288|611;260	.|ENSP00000336923:V611M;ENSP00000406624:V260M	.|ENSP00000336923:V611M	R|V	+|+	2|1	0|0	ARHGAP10|ARHGAP10	149163978|149163978	0.951000|0.951000	0.32395|0.32395	0.938000|0.938000	0.37757|0.37757	0.989000|0.989000	0.77384|0.77384	1.511000|1.511000	0.35801|0.35801	0.732000|0.732000	0.32470|0.32470	0.655000|0.655000	0.94253|0.94253	CGT|GTG		TCGA-IB-A5SQ-01A-11D-A32N-08	ARHGAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365005.1	1	0	0	31	397	0	79	1	7.471434e-01	5	31	0	79	2		0	0	0	0	0	2	1	1.000000	31	389	0	78	2	0	0	0	0	0	0		-8.500285	1	1	121412	4	40	1	1	2	3	2.018787	0	0.150000	1.900000	0.154439	0.980000	0.680000	1.000000	1.000000	0.929418	0.980000	1	0.810000	1.000000
QDPR	5860	broad.mit.edu	37	4	17488811	17488811	+	Silent	SNP	G	G	A			TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr4:17488811G>A	ENST00000281243.5	-	7	857	c.678C>T	c.(676-678)agC>agT	p.S226S	QDPR_ENST00000428702.2_Silent_p.S195S|QDPR_ENST00000513615.1_3'UTR|QDPR_ENST00000508623.1_Missense_Mutation_p.A162V	NM_000320.2	NP_000311.2	P09417	DHPR_HUMAN	quinoid dihydropteridine reductase			13					CCTGGATTAGGCTTCCTGAGC	0.453000																								0							SO:0001819	synonymous_variant			ENST00000281243.5	1	1	hg19	CCDS3421.1	.	.	.	.	.	.	.	.	.	.	G	13.30	2.196879	0.38806	.	.	ENSG00000151552	ENST00000508623	D	0.92699	-3.09	5.29	3.56	0.40772	.	.	.	.	.	D	0.90648	0.7067	.	.	.	0.23260	N	0.998021	.	.	.	.	.	.	D	0.84350	0.0532	6	0.87932	D	0	-26.8617	5.9529	0.19257	0.3459:0.0:0.6541:0.0	.	.	.	.	V	162	ENSP00000426377:A162V	ENSP00000426377:A162V	A	-	2	0	QDPR	17097909	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	0.824000	0.27379	1.237000	0.43756	0.650000	0.86243	GCC		TCGA-IB-A5SQ-01A-11D-A32N-08	QDPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250372.1	0	0	0	27	361	0	88	1	1	22	369	0	88	2		0	0	0	0	0	2	1	1.000000	27	356	0	87	2	0	0	0	0	0	0		-7.449956	1	1	0	0		1	1	2	3	2.018787	0	0.150000	1.900000	0.154439	0.940000	0.630000	1.000000	1.000000	0.907192	0.940000	1	0.770000	1.000000
KIAA1211	57482	broad.mit.edu	37	4	57180336	57180336	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr4:57180336G>A	ENST00000504228.1	+	6	773	c.668G>A	c.(667-669)cGc>cAc	p.R223H	KIAA1211_ENST00000264229.6_Missense_Mutation_p.R223H|KIAA1211_ENST00000541073.1_Missense_Mutation_p.R216H			Q6ZU35	K1211_HUMAN	KIAA1211			65	Glioma(25;0.08)|all_neural(26;0.101)				GAGAGAAGACGCCAAGAAGAC	0.612000																								0							SO:0001583	missense			ENST00000504228.1	0	1	hg19	CCDS43230.1	.	.	.	.	.	.	.	.	.	.	G	9.671	1.146801	0.21288	.	.	ENSG00000109265	ENST00000264229;ENST00000504228;ENST00000541073;ENST00000546221	T;T;T	0.12255	2.7;2.7;2.7	5.07	-0.161	0.13371	.	.	.	.	.	T	0.07683	0.0193	L	0.44542	1.39	0.09310	N	1	B;B;B	0.29612	0.251;0.022;0.022	B;B;B	0.20767	0.031;0.007;0.007	T	0.36553	-0.9743	9	0.17369	T	0.5	-5.3546	0.3015	0.00274	0.2693:0.1396:0.2867:0.3044	.	216;216;223	B7ZVZ4;F5H1N7;Q6ZU35	.;.;K1211_HUMAN	H	223;223;216;133	ENSP00000264229:R223H;ENSP00000423366:R223H;ENSP00000444006:R216H	ENSP00000264229:R223H	R	+	2	0	KIAA1211	56875093	0.000000	0.05858	0.160000	0.22671	0.856000	0.48823	0.263000	0.18478	0.225000	0.20959	0.561000	0.74099	CGC		TCGA-IB-A5SQ-01A-11D-A32N-08	KIAA1211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362097.2	0	0	0	6	97	0	17	1	3.801046e-01	3	17	0	17	2		0	0	0	0	0	2	1	0.964328	6	95	0	17	2	0	0	0	0	0	0		-4.745202	1	1	0	0		1	1	2	3	2.018787	0	0.150000	1.900000	0.154439	0.830000	0.350000	1.000000	1.000000	0.793932	0.830000	0	0.550000	1.000000
TMPRSS11F	389208	broad.mit.edu	37	4	68995528	68995528	+	Splice_Site	SNP	G	G	A	rs142296401	byFrequency	TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr4:68995528G>A	ENST00000356291.2	-	1	70	c.11C>T	c.(10-12)gCa>gTa	p.A4V		NM_207407.2	NP_997290.2	Q6ZWK6	TM11F_HUMAN	transmembrane protease, serine 11F			39					GAATACTTACGCGTACATCAT	0.448000																								0							SO:0001630	splice_region_variant			ENST00000356291.2	1	0	hg19	CCDS3520.1	.	.	.	.	.	.	.	.	.	.	G	11.84	1.759073	0.31137	0.001589	0.0	ENSG00000198092	ENST00000356291	D	0.88509	-2.39	5.24	3.48	0.39840	.	1.880980	0.02227	N	0.064593	T	0.78748	0.4332	N	0.08118	0	0.34127	D	0.6648	P	0.48089	0.905	B	0.35770	0.21	T	0.70174	-0.4944	9	.	.	.	.	11.8719	0.52525	0.0:0.3399:0.6601:0.0	.	4	Q6ZWK6	TM11F_HUMAN	V	4	ENSP00000348639:A4V	.	A	-	2	0	TMPRSS11F	68678123	0.951000	0.32395	0.948000	0.38648	0.344000	0.29017	0.715000	0.25822	0.756000	0.33013	0.650000	0.86243	GCA		TCGA-IB-A5SQ-01A-11D-A32N-08	TMPRSS11F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251439.1	1	0	0	24	298	0	55		0	0	0	0	55	2		0	0	0	0	0	2	1	1.000000	24	294	0	53	2	0	0	0	0	0	0		-3.221880	1	1	121412	25	46	1	1	2	3	2.018787	0	0.150000	1.900000	0.154439	0.990000	0.660000	1.000000	1.000000	0.934857	0.990000	1	0.820000	1.000000
NSD1	64324	broad.mit.edu	37	5	176562809	176562809	+	Silent	SNP	A	A	G			TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr5:176562809A>G	ENST00000439151.2	+	2	750	c.705A>G	c.(703-705)acA>acG	p.T235T	NSD1_ENST00000361032.4_Silent_p.T235T|NSD1_ENST00000347982.4_Intron|NSD1_ENST00000354179.4_Intron|NSD1_ENST00000511258.1_Intron	NM_022455.4	NP_071900.2	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1			96	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)		AGACTGAAACACAGAAAAATA	0.458000			T	NUP98	AML		Sotos Syndrome		Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome	HNSCC(47;0.14)					Dom	yes		5	5q35	64324	nuclear receptor binding SET domain protein 1	yes	L	0							SO:0001819	synonymous_variant	Familial Cancer Database	Weaver-Smith syndrome;Cerebral Gigantism;BWS, Exomphalos-Macroglossia-Gigantism (EMG) syndrome, Wiedemann-Beckwith syndrome, WBS	ENST00000439151.2	1	1	hg19	CCDS4412.1																																																																																				TCGA-IB-A5SQ-01A-11D-A32N-08	NSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253412.2	1	0	0	25	283	0	45	0	6.062986e-02	0	5	0	45	2		0	0	0	0	0	2	1	1.000000	25	281	0	45	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	1	2	3	2.015147	0	0.150000	1.900000	0.153176	0.990000	0.730000	1.000000	1.000000	0.962778	0.990000	1	0.890000	1.000000
DDX41	51428	broad.mit.edu	37	5	176941738	176941738	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr5:176941738C>T	ENST00000507955.1	-	9	1422	c.899G>A	c.(898-900)gGc>gAc	p.G300D	DDX41_ENST00000506965.1_5'Flank	NM_016222.2	NP_057306.2	Q9UJV9	DDX41_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 41				all_cancers(89;0.00033)|Renal(175;0.000269)|Lung NSC(126;0.00161)|all_lung(126;0.00286)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.191)		CACGGACATGCCCCCAATGCA	0.637000																								0							SO:0001583	missense			ENST00000507955.1	0	1	hg19	CCDS4427.1	.	.	.	.	.	.	.	.	.	.	C	27.0	4.795543	0.90453	.	.	ENSG00000183258	ENST00000330503;ENST00000507955	T;T	0.50548	0.74;0.74	5.74	4.85	0.62838	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.056454	0.64402	N	0.000001	T	0.76026	0.3930	M	0.92880	3.355	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.83210	-0.0074	10	0.87932	D	0	-27.0527	15.8993	0.79359	0.1364:0.8636:0.0:0.0	.	174;300	B3KRK2;Q9UJV9	.;DDX41_HUMAN	D	318;300	ENSP00000330349:G318D;ENSP00000422753:G300D	ENSP00000330349:G318D	G	-	2	0	DDX41	176874344	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.351000	0.79395	1.378000	0.46305	0.655000	0.94253	GGC		TCGA-IB-A5SQ-01A-11D-A32N-08	DDX41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253432.2	0	0	0	7	900	1	194	0	2.665377e-02	0	114	1	194	4		0	0	0	0	0	2	0	0.029225	7	891	1	190	17	0	0	0	0	0	0		-1.680598	0	1	0	0		1	1	2	3	2.015147	0	0.150000	1.900000	0.153176	0.100000	0.040000	1.000000	0.100000	0.150595	0.100000	0	0.070000	0.170000
FLT4	2324	broad.mit.edu	37	5	180056983	180056983	+	Missense_Mutation	SNP	G	G	T			TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr5:180056983G>T	ENST00000261937.6	-	5	714	c.636C>A	c.(634-636)gaC>gaA	p.D212E	FLT4_ENST00000424276.2_5'UTR|FLT4_ENST00000502649.1_Missense_Mutation_p.D212E|FLT4_ENST00000393347.3_Missense_Mutation_p.D212E	NM_182925.4	NP_891555.2	P35916	VGFR3_HUMAN	fms-related tyrosine kinase 4			71	all_cancers(89;2.21e-05)|all_epithelial(37;5.29e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00245)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	GGAAGTCCTGGTCTCCCCAGG	0.637000													Colon(97;1075 1466 27033 27547 35871)											0							SO:0001583	missense			ENST00000261937.6	0	1	hg19	CCDS4457.1	.	.	.	.	.	.	.	.	.	.	G	12.80	2.047952	0.36085	.	.	ENSG00000037280	ENST00000261937;ENST00000393347;ENST00000502649;ENST00000376868	T;T;T	0.04654	3.58;3.58;3.58	5.06	4.17	0.49024	Tyrosine-protein kinase, vascular endothelial growth factor receptor 3 (VEGFR3), N-terminal (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.03783	0.0107	L	0.34521	1.04	0.28658	N	0.906316	B;P;B;B	0.35033	0.349;0.481;0.003;0.003	B;B;B;B	0.33454	0.05;0.164;0.004;0.004	T	0.27262	-1.0079	9	0.30078	T	0.28	.	3.8203	0.08833	0.09:0.1755:0.576:0.1585	.	212;212;212;212	B5A927;P35916-3;E9PD35;P35916	.;.;.;VGFR3_HUMAN	E	212;212;212;22	ENSP00000261937:D212E;ENSP00000377016:D212E;ENSP00000426057:D212E	ENSP00000261937:D212E	D	-	3	2	FLT4	179989589	1.000000	0.71417	0.996000	0.52242	0.848000	0.48234	2.115000	0.41921	2.517000	0.84864	0.561000	0.74099	GAC		TCGA-IB-A5SQ-01A-11D-A32N-08	FLT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253527.4	0	0	0	5	287	0	62	0	1.537802e-02	0	9	0	62	2		0	0	0	0	0	2	0	0.934606	1	285	0	62	2	0	0	0	0	0	0		-6.328591	1	0	0	0		1	1	2	3	2.015147	0	0.150000	1.900000	0.153176	0.250000	0.090000	1.000000	0.230000	0.295774	0.250000	0	0.150000	0.390000
BCLAF1	9774	broad.mit.edu	37	6	136589449	136589449	+	Nonsense_Mutation	SNP	G	G	A	rs147719127		TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr6:136589449G>A	ENST00000531224.1	-	10	2500	c.2248C>T	c.(2248-2250)Cga>Tga	p.R750*	BCLAF1_ENST00000527536.1_Nonsense_Mutation_p.R750*|BCLAF1_ENST00000353331.4_Nonsense_Mutation_p.R748*|BCLAF1_ENST00000527759.1_Nonsense_Mutation_p.R748*|BCLAF1_ENST00000530767.1_Nonsense_Mutation_p.R577*|BCLAF1_ENST00000392348.2_Nonsense_Mutation_p.R748*|BCLAF1_ENST00000031135.9_5'UTR|BCLAF1_ENST00000529917.1_5'UTR	NM_001077441.1|NM_014739.2	NP_001070909.1|NP_055554.1	Q9NYF8	BCLF1_HUMAN	BCL2-associated transcription factor 1	p.R750G(1)		9	Colorectal(23;0.24)				GATGAAGATCGAGAATGATCT	0.338000													Colon(142;1534 1789 5427 7063 28491)											1	Substitution - Missense(1)						SO:0001587	stop_gained			ENST00000531224.1	0	1	hg19	CCDS5177.1	.	.	.	.	.	.	.	.	.	.	G	42	9.204499	0.99099	0.0	5.81E-4	ENSG00000029363	ENST00000531224;ENST00000353331;ENST00000527536;ENST00000530767;ENST00000527759;ENST00000392348	.	.	.	4.97	4.07	0.47477	.	0.000000	0.47852	D	0.000213	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.7893	12.524	0.56075	0.0:0.0:0.612:0.388	.	.	.	.	X	750;748;750;577;748;748	.	ENSP00000229446:R748X	R	-	1	2	BCLAF1	136631142	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.833000	0.39161	1.190000	0.43042	0.484000	0.47621	CGA		TCGA-IB-A5SQ-01A-11D-A32N-08	BCLAF1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042375.2	0	0	0	10	250	0	47	0	7.215952e-01	0	64	0	47	2		0	0	0	0	0	2	1	0.995104	8	227	0	47	2	0	0	0	0	0	0		-2.548925	1	1	121386	112	46	1	0	0	0	1.973124	0	0.150000	1.900000	0.127758	0.500000	0.260000	0.850000	0.500000	0.530818	0.500000	0	0.370000	0.680000
OR10C1	442194	broad.mit.edu	37	6	29408019	29408019	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr6:29408019C>T	ENST00000444197.2	+	1	937	c.227C>T	c.(226-228)aCg>aTg	p.T76M	OR11A1_ENST00000377149.1_Intron	NM_013941.3	NP_039229.3	Q96KK4	O10C1_HUMAN	olfactory receptor, family 10, subfamily C, member 1 (gene/pseudogene)			27					ACGTCTGTCACGGTCCCCCTG	0.577000																								0							SO:0001583	missense			ENST00000444197.2	1	1	hg19	CCDS34364.1	.	.	.	.	.	.	.	.	.	.	C	7.874	0.728727	0.15507	.	.	ENSG00000206474	ENST00000444197	T	0.00882	5.58	3.32	3.32	0.38043	GPCR, rhodopsin-like superfamily (1);	0.000000	0.40302	N	0.001132	T	0.01940	0.0061	M	0.88570	2.965	0.09310	N	0.999996	D	0.69078	0.997	P	0.61722	0.893	T	0.38090	-0.9677	10	0.52906	T	0.07	.	6.6195	0.22796	0.0:0.8667:0.0:0.1333	.	76	Q96KK4	O10C1_HUMAN	M	76	ENSP00000419119:T76M	ENSP00000419119:T76M	T	+	2	0	OR10C1	29515998	0.000000	0.05858	0.287000	0.24848	0.043000	0.13939	-0.103000	0.10940	1.858000	0.53909	0.196000	0.17591	ACG		TCGA-IB-A5SQ-01A-11D-A32N-08	OR10C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076415.2	1	0	0	38	516	0	114		0	0	0	0	114	2		0	0	0	0	0	2	1	1.000000	38	512	0	112	2	0	0	0	0	0	0		-8.383347	1	1	0	0		1	0	0	0	1.988739	0	0.150000	1.900000	0.135740	0.890000	0.640000	1.000000	1.000000	0.886146	0.890000	1	0.760000	1.000000
MAS1L	116511	broad.mit.edu	37	6	29454889	29454889	+	Missense_Mutation	SNP	G	G	A	rs145448286	byFrequency	TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr6:29454889G>A	ENST00000377127.3	-	1	849	c.791C>T	c.(790-792)gCg>gTg	p.A264V		NM_052967.1	NP_443199.1	P35410	MAS1L_HUMAN	MAS1 proto-oncogene like, G protein-coupled receptor			28					CTGCACCACCGCATAGACCCT	0.522000													NSCLC(153;755 1987 3859 11251 32945)											0							SO:0001583	missense			ENST00000377127.3	0	1	hg19	CCDS4661.1	.	.	.	.	.	.	.	.	.	.	G	2.332	-0.353156	0.05173	0.001135	0.0	ENSG00000204687	ENST00000377127	T	0.36340	1.26	2.23	-3.69	0.04450	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.01592	0.0051	N	0.00510	-1.415	0.09310	N	1	B	0.25390	0.125	B	0.25291	0.059	T	0.32561	-0.9902	9	0.02654	T	1	.	3.4815	0.07603	0.5201:0.2028:0.2771:0.0	.	264	P35410	MAS1L_HUMAN	V	264	ENSP00000366331:A264V	ENSP00000366331:A264V	A	-	2	0	MAS1L	29562868	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.366000	0.01078	-0.792000	0.04480	-0.451000	0.05528	GCG		TCGA-IB-A5SQ-01A-11D-A32N-08	MAS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076126.2	0	0	0	4	216	0	33	0	0	0	1	0	33	2		0	0	0	0	0	2	1	0.890095	4	215	0	33	2	0	0	0	0	0	0		-3.480473	1	1	121410	14	40	1	0	0	0	1.988739	0	0.150000	1.900000	0.135740	0.260000	0.080000	0.550000	0.230000	0.286831	0.260000	0	0.150000	0.400000
PRPH2	5961	broad.mit.edu	37	6	42689575	42689575	+	Silent	SNP	G	G	A			TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr6:42689575G>A	ENST00000230381.5	-	1	737	c.498C>T	c.(496-498)tgC>tgT	p.C166C		NM_000322.4	NP_000313.2	P23942	PRPH2_HUMAN	peripherin 2 (retinal degeneration, slow)			18	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.00178)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.0904)		CGTTGTTGCCGCAGCATTTGA	0.507000																								0							SO:0001819	synonymous_variant			ENST00000230381.5	0	1	hg19	CCDS4871.1																																																																																				TCGA-IB-A5SQ-01A-11D-A32N-08	PRPH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040556.1	0	0	0	6	566	0	102	0	0	0	1	0	102	2		0	0	0	0	0	2	1	0.963771	6	559	0	102	2	0	0	0	0	0	0		-1.878624	0	1	121412	9	44	1	0	0	0	1.973124	0	0.150000	1.900000	0.127758	0.140000	0.050000	0.280000	0.130000	0.156568	0.140000	0	0.090000	0.210000
CAPN11	11131	broad.mit.edu	37	6	44144381	44144381	+	Silent	SNP	C	C	T			TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr6:44144381C>T	ENST00000398776.1	+	10	1103	c.1065C>T	c.(1063-1065)gaC>gaT	p.D355D	CAPN11_ENST00000542245.1_Silent_p.D355D	NM_007058.3	NP_008989.2	Q9UMQ6	CAN11_HUMAN	calpain 11			36	all_cancers(18;3.19e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)		AGACGGAGGACGGGGAGTTCT	0.627000																								0							SO:0001819	synonymous_variant			ENST00000398776.1	1	1	hg19	CCDS47436.1																																																																																				TCGA-IB-A5SQ-01A-11D-A32N-08	CAPN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040714.3	1	0	0	28	322	0	57	0	0	0	1	0	57	2		0	0	0	0	0	2	1	1.000000	28	315	0	56	2	0	0	0	0	0	0		-9.122323	1	1	121066	7	40	1	0	0	0	1.973124	0	0.150000	1.900000	0.127758	0.990000	0.700000	1.000000	1.000000	0.949246	0.990000	1	0.850000	1.000000
TNFRSF21	27242	broad.mit.edu	37	6	47253929	47253929	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr6:47253929G>A	ENST00000296861.2	-	2	892	c.499C>T	c.(499-501)Cgg>Tgg	p.R167W		NM_014452.3	NP_055267.1	O75509	TNR21_HUMAN	tumor necrosis factor receptor superfamily, member 21			21			Lung(136;0.189)		TGCTTACACCGCACATCCTCA	0.542000																								0							SO:0001583	missense			ENST00000296861.2	0	1	hg19	CCDS4921.1	.	.	.	.	.	.	.	.	.	.	G	18.65	3.668949	0.67814	.	.	ENSG00000146072	ENST00000296861	T	0.61742	0.08	5.54	4.61	0.57282	TNFR/CD27/30/40/95 cysteine-rich region (1);	0.164121	0.49305	D	0.000156	T	0.65154	0.2664	M	0.72894	2.215	0.47214	D	0.999353	D	0.89917	1.0	P	0.62649	0.905	T	0.68108	-0.5496	10	0.72032	D	0.01	.	12.0809	0.53669	0.0:0.0:0.6729:0.327	.	167	O75509	TNR21_HUMAN	W	167	ENSP00000296861:R167W	ENSP00000296861:R167W	R	-	1	2	TNFRSF21	47361888	0.996000	0.38824	1.000000	0.80357	0.997000	0.91878	2.334000	0.43920	2.767000	0.95098	0.591000	0.81541	CGG		TCGA-IB-A5SQ-01A-11D-A32N-08	TNFRSF21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040814.1	0	0	0	8	625	0	146	0	9.546107e-01	0	424	0	146	2		0	0	0	0	0	2	1	0.988868	8	618	0	144	2	0	0	0	0	0	0		-1.909332	0	1	121412	5	40	1	0	0	0	1.973124	0	0.150000	1.900000	0.127758	0.170000	0.070000	0.310000	0.160000	0.182175	0.170000	0	0.110000	0.240000
EPHA1	2041	broad.mit.edu	37	7	143096794	143096794	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr7:143096794C>T	ENST00000275815.3	-	4	871	c.785G>A	c.(784-786)tGc>tAc	p.C262Y		NM_005232.4	NP_005223.4	P21709	EPHA1_HUMAN	EPH receptor A1			51	Melanoma(164;0.205)	Myeloproliferative disorder(862;0.0255)			CTCACAGTGGCACCGTCCTAC	0.652000																								0							SO:0001583	missense			ENST00000275815.3	1	1	hg19	CCDS5884.1	.	.	.	.	.	.	.	.	.	.	C	19.71	3.877639	0.72294	.	.	ENSG00000146904	ENST00000275815	D	0.86627	-2.15	5.22	4.33	0.51752	Tyrosine-protein kinase, receptor class V, conserved site (1);Growth factor, receptor (1);	0.000000	0.64402	D	0.000003	D	0.92652	0.7665	M	0.93978	3.48	0.49213	D	0.999766	D	0.58970	0.984	P	0.51550	0.673	D	0.94170	0.7422	10	0.87932	D	0	.	13.6352	0.62219	0.0:0.926:0.0:0.074	.	262	P21709	EPHA1_HUMAN	Y	262	ENSP00000275815:C262Y	ENSP00000275815:C262Y	C	-	2	0	EPHA1	142806916	1.000000	0.71417	0.986000	0.45419	0.907000	0.53573	7.518000	0.81795	1.409000	0.46915	0.655000	0.94253	TGC		TCGA-IB-A5SQ-01A-11D-A32N-08	EPHA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342154.1	1	0	0	35	402	0	74	1	1.083411e-01	4	3	0	74	2		0	0	0	0	0	2	1	1.000000	34	397	0	70	2	0	0	0	0	0	0		-3.221884	1	1	0	0		1	2	2	4	2.158698	1	0.150000	1.900000	0.210404	0.990000	0.840000	1.000000	1.000000	0.987438	0.990000	1	0.990000	1.000000
DNAH11	8701	broad.mit.edu	37	7	21882220	21882220	+	Missense_Mutation	SNP	C	C	G			TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr7:21882220C>G	ENST00000409508.3	+	66	10781	c.10750C>G	c.(10750-10752)Cac>Gac	p.H3584D	DNAH11_ENST00000328843.6_Missense_Mutation_p.H3591D	NM_001277115.1	NP_001264044.1	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11			230					CCTTATCCTTCACACAAAATT	0.413000									Kartagener syndrome															0							SO:0001583	missense	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	ENST00000409508.3	1	1	hg19		.	.	.	.	.	.	.	.	.	.	C	17.85	3.490687	0.64074	.	.	ENSG00000105877	ENST00000328843	T	0.23348	1.91	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	T	0.53061	0.1773	.	.	.	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.53634	-0.8411	9	0.52906	T	0.07	.	17.8716	0.88813	0.0:1.0:0.0:0.0	.	3591	Q96DT5	DYH11_HUMAN	D	3591	ENSP00000330671:H3591D	ENSP00000330671:H3591D	H	+	1	0	DNAH11	21848745	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.811000	0.86092	2.514000	0.84764	0.655000	0.94253	CAC		TCGA-IB-A5SQ-01A-11D-A32N-08	DNAH11-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000326582.6	0	0	0	12	181	0	28		0	0	0	0	28	2		0	0	0	0	0	2	1	0.999129	12	178	0	28	2	0	0	0	0	0	0		-3.145372	1	1	0	0		1	0	1	1	2.010727	0	0.150000	1.900000	0.145514	0.830000	0.460000	1.000000	1.000000	0.817277	0.830000	0	0.620000	1.000000
FAM135B	51059	broad.mit.edu	37	8	139165382	139165382	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr8:139165382C>T	ENST00000395297.1	-	13	1506	c.1336G>A	c.(1336-1338)Gat>Aat	p.D446N		NM_015912.3	NP_056996.2	Q49AJ0	F135B_HUMAN	family with sequence similarity 135, member B			238	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)		ATACAGTTATCTTCCTTGTCT	0.328000										HNSCC(54;0.14)														0							SO:0001583	missense			ENST00000395297.1	1	1	hg19	CCDS6375.2	.	.	.	.	.	.	.	.	.	.	C	2.542	-0.306135	0.05458	.	.	ENSG00000147724	ENST00000395297	T	0.13778	2.56	5.6	3.44	0.39384	.	2.006110	0.01697	N	0.026948	T	0.10895	0.0266	N	0.19112	0.55	0.09310	N	1	B;B;B	0.29805	0.257;0.157;0.094	B;B;B	0.26864	0.074;0.051;0.023	T	0.28427	-1.0044	10	0.17369	T	0.5	-5.0172	10.0861	0.42419	0.0:0.8112:0.0:0.1888	.	446;446;446	Q49AJ0-3;Q49AJ0-4;Q49AJ0	.;.;F135B_HUMAN	N	446	ENSP00000378710:D446N	ENSP00000276737:D446N	D	-	1	0	FAM135B	139234564	0.831000	0.29352	0.867000	0.34043	0.006000	0.05464	2.266000	0.43320	1.348000	0.45733	0.655000	0.94253	GAT		TCGA-IB-A5SQ-01A-11D-A32N-08	FAM135B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313590.3	1	0	0	20	227	0	31	0	2.090491e-02	0	3	0	31	2		0	0	0	0	0	2	1	0.999996	20	227	0	31	2	0	0	0	0	0	0		-7.942450	1	1	0	0		1	2	2	4	2.322096	1	0.150000	1.900000	0.260870	0.990000	0.790000	1.000000	1.000000	0.983884	0.990000	1	0.990000	1.000000
PLEC	5339	broad.mit.edu	37	8	144996470	144996470	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr8:144996470G>A	ENST00000322810.4	-	32	8099	c.7930C>T	c.(7930-7932)Cgc>Tgc	p.R2644C	PLEC_ENST00000436759.2_Missense_Mutation_p.R2534C|PLEC_ENST00000354589.3_Missense_Mutation_p.R2507C|PLEC_ENST00000527096.1_Missense_Mutation_p.R2530C|PLEC_ENST00000357649.2_Missense_Mutation_p.R2511C|PLEC_ENST00000354958.2_Missense_Mutation_p.R2485C|PLEC_ENST00000345136.3_Missense_Mutation_p.R2507C|PLEC_ENST00000356346.3_Missense_Mutation_p.R2493C|PLEC_ENST00000398774.2_Missense_Mutation_p.R2475C	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin			137					TCGATGAAGCGCTCCCGCTGT	0.627000																								0							SO:0001583	missense			ENST00000322810.4	1	1	hg19	CCDS43772.1	.	.	.	.	.	.	.	.	.	.	g	10.43	1.349012	0.24426	.	.	ENSG00000178209	ENST00000345136;ENST00000357649;ENST00000354589;ENST00000398774;ENST00000322810;ENST00000354958;ENST00000356346;ENST00000436759;ENST00000527096	T;T;T;T;T;T;T;T;T	0.78595	-1.16;-1.16;-1.19;-1.19;-1.17;-1.16;-1.15;-1.16;-1.16	4.38	4.38	0.52667	.	0.100263	0.38720	U	0.001592	T	0.68979	0.3060	L	0.40543	1.245	0.50039	D	0.999843	D;D;D;D;D;D;D;D	0.60160	0.987;0.987;0.987;0.978;0.987;0.987;0.987;0.987	B;B;B;B;B;B;B;B	0.42882	0.401;0.401;0.401;0.226;0.401;0.401;0.401;0.401	T	0.73697	-0.3901	10	0.87932	D	0	.	10.1728	0.42920	0.0:0.0:0.6587:0.3413	.	2534;2493;2485;2644;2475;2507;2511;2507	Q15149-2;Q15149-9;Q15149-8;Q15149;Q15149-7;Q15149-5;Q15149-6;Q15149-4	.;.;.;PLEC_HUMAN;.;.;.;.	C	2507;2511;2507;2475;2644;2485;2493;2534;2530	ENSP00000344848:R2507C;ENSP00000350277:R2511C;ENSP00000346602:R2507C;ENSP00000381756:R2475C;ENSP00000323856:R2644C;ENSP00000347044:R2485C;ENSP00000348702:R2493C;ENSP00000388180:R2534C;ENSP00000434583:R2530C	ENSP00000323856:R2644C	R	-	1	0	PLEC	145068458	0.964000	0.33143	0.950000	0.38849	0.712000	0.41017	2.523000	0.45580	2.289000	0.77006	0.443000	0.29094	CGC		TCGA-IB-A5SQ-01A-11D-A32N-08	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	1	0	1	23	190	0	27	1	9.999991e-01	69	130	0	27	2		0	0	0	0	0	2	1	1.000000	23	187	0	27	2	0	0	0	0	0	0		-20.000000	1	1	121096	3	30	1	2	2	4	2.322096	1	0.150000	1.900000	0.260870	0.990000	0.990000	1.000000	1.000000	0.999388	0.990000	1	0.990000	1.000000
DCAF4L2	138009	broad.mit.edu	37	8	88885063	88885063	+	Silent	SNP	T	T	C			TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr8:88885063T>C	ENST00000319675.3	-	1	1233	c.1137A>G	c.(1135-1137)ccA>ccG	p.P379P		NM_152418.3	NP_689631.1	Q8NA75	DC4L2_HUMAN	DDB1 and CUL4 associated factor 4-like 2			83					TGAGCAGCCCTGGTGCTCCTC	0.562000																								0							SO:0001819	synonymous_variant			ENST00000319675.3	1	1	hg19	CCDS6245.1																																																																																				TCGA-IB-A5SQ-01A-11D-A32N-08	DCAF4L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375302.1	1	0	1	50	323	0	50		0	0	0	0	50	2		0	0	0	0	0	2	1	1.000000	48	320	0	50	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	1	2	3	2.038737	0	0.150000	1.900000	0.184261	0.990000	0.990000	1.000000	1.000000	1.000000	0.990000	1	0.990000	1.000000
DBH	1621	broad.mit.edu	37	9	136508639	136508639	+	Silent	SNP	C	C	T	rs78200745		TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr9:136508639C>T	ENST00000393056.2	+	4	861	c.849C>T	c.(847-849)tgC>tgT	p.C283C		NM_000787.3	NP_000778.3	P09172	DOPO_HUMAN	dopamine beta-hydroxylase (dopamine beta-monooxygenase)			36				Disulfiram(DB00822)|Dopamine(DB00988)|Propylthiouracil(DB00550)|Vitamin C(DB00126)	GCGGGCCCTGCGACTCCAAGA	0.662000																								0							SO:0001819	synonymous_variant			ENST00000393056.2	0	1	hg19	CCDS6977.2																																																																																				TCGA-IB-A5SQ-01A-11D-A32N-08	DBH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054929.2	0	0	0	5	481	0	78		0	0	0	0	78	2		0	0	0	0	0	2	1	0.935431	5	474	0	78	2	0	0	0	0	0	0		-2.758927	1	1	121408	39	47	1	1	2	3	2.057426	0	0.150000	1.900000	0.162562	0.160000	0.050000	1.000000	0.130000	0.291276	0.160000	0	0.090000	0.360000
SEC16A	9919	broad.mit.edu	37	9	139360502	139360502	+	Silent	SNP	G	G	A			TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr9:139360502G>A	ENST00000371706.3	-	6	3714	c.3681C>T	c.(3679-3681)taC>taT	p.Y1227Y	SEC16A_ENST00000431893.2_Silent_p.Y1227Y|SEC16A_ENST00000290037.6_Silent_p.Y1227Y|SEC16A_ENST00000313050.7_Silent_p.Y1405Y			O15027	SC16A_HUMAN	SEC16 homolog A (S. cerevisiae)			51		Myeloproliferative disorder(178;0.0511)			GGTAGGTGCCGTAGGCAAAAT	0.577000																								0							SO:0001819	synonymous_variant			ENST00000371706.3	0	1	hg19		.	.	.	.	.	.	.	.	.	.	G	0.575	-0.839346	0.02692	0.0	2.38E-4	ENSG00000148396	ENST00000433860	.	.	.	5.76	-0.351	0.12602	.	.	.	.	.	T	0.56046	0.1959	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.51028	-0.8757	4	.	.	.	-24.8088	9.9193	0.41455	0.5084:0.0:0.4916:0.0	.	.	.	.	W	102	.	.	R	-	1	2	SEC16A	138480323	0.021000	0.18746	0.099000	0.21106	0.012000	0.07955	-0.799000	0.04560	0.080000	0.16959	-0.136000	0.14681	CGG		TCGA-IB-A5SQ-01A-11D-A32N-08	SEC16A-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000055077.1	0	0	0	5	559	0	114	0	6.645505e-02	0	38	0	114	2		0	0	0	0	0	2	1	0.933261	5	544	0	113	2	0	0	0	0	0	0		-2.450970	0	1	120944	47	49	1	1	2	3	2.057426	0	0.150000	1.900000	0.162562	0.140000	0.040000	1.000000	0.120000	0.272206	0.140000	0	0.080000	0.310000
TRO	7216	broad.mit.edu	37	X	54957327	54957327	+	Silent	SNP	G	G	A			TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chrX:54957327G>A	ENST00000173898.7	+	12	4282	c.4170G>A	c.(4168-4170)ccG>ccA	p.P1390P	TRO_ENST00000420798.2_Silent_p.P921P|TRO_ENST00000375022.4_Intron|TRO_ENST00000399736.1_Intron|TRO_ENST00000375041.2_Silent_p.P993P|TRO_ENST00000319167.8_Intron	NM_001039705.2	NP_001034794.1	Q12816	TROP_HUMAN	trophinin			37					GCGGTGGACCGAGCACAGGAG	0.602000																								0							SO:0001819	synonymous_variant			ENST00000173898.7	1	1	hg19	CCDS43959.1																																																																																				TCGA-IB-A5SQ-01A-11D-A32N-08	TRO-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056837.3	0	0	0	28	547	1	111	0	3.264240e-01	0	38	1	111	3		0	0	0	0	0	2	1	1.000000	28	537	0	109	2	0	0	0	0	0	0		-2.774557	1	1	121060	1	31	1	0	1	1			0.150000	1.900000	0.150000	0.650000	0.440000	0.900000	0.640000	0.663226	0.650000	0	0.530000	0.780000
AR	367	broad.mit.edu	37	X	66765211	66765211	+	Missense_Mutation	SNP	C	C	G			TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chrX:66765211C>G	ENST00000374690.3	+	1	747	c.223C>G	c.(223-225)Cag>Gag	p.Q75E	AR_ENST00000513847.1_3'UTR|AR_ENST00000396044.3_Missense_Mutation_p.Q75E|AR_ENST00000504326.1_Missense_Mutation_p.Q75E	NM_000044.3	NP_000035.2	P10275	ANDR_HUMAN	androgen receptor			67	all_cancers(1;0.173)|Prostate(1;2.27e-16)|all_epithelial(1;0.102)	all_lung(315;1.3e-11)		Bicalutamide(DB01128)|Cyproterone acetate(DB04839)|Danazol(DB01406)|Drospirenone(DB01395)|Drostanolone(DB00858)|Enzalutamide(DB08899)|Fludrocortisone(DB00687)|Fluoxymesterone(DB01185)|Flutamide(DB00499)|Ketoconazole(DB01026)|Levonorgestrel(DB00367)|Methyltestosterone(DB06710)|Nandrolone decanoate(DB08804)|Nandrolone phenpropionate(DB00984)|Nilutamide(DB00665)|Oxandrolone(DB00621)|Spironolactone(DB00421)|Testosterone Propionate(DB01420)|Testosterone(DB00624)	gcagcagcagcagcagcagca	0.667000									Androgen Insensitivity Syndrome															0							SO:0001583	missense	Familial Cancer Database	CAIS, Testicular Feminisation, AIS, Morris syndrome; incl. Reifenstein Syndrome	ENST00000374690.3	1	0	hg19	CCDS14387.1	.	.	.	.	.	.	.	.	.	.	N	11.10	1.538273	0.27475	.	.	ENSG00000169083	ENST00000374690;ENST00000504326;ENST00000396044	T;T;T	0.78924	-1.22;-1.22;-1.22	3.02	3.02	0.34903	.	.	.	.	.	D	0.87549	0.6205	M	0.88640	2.97	0.18873	N	0.999986	D;P;P	0.59357	0.985;0.843;0.529	D;P;B	0.73708	0.981;0.848;0.363	T	0.75988	-0.3123	9	0.35671	T	0.21	.	8.7659	0.34702	0.0:1.0:0.0:0.0	.	75;75;73	E7EVX6;D3YPQ2;P10275	.;.;ANDR_HUMAN	E	75	ENSP00000363822:Q75E;ENSP00000421155:Q75E;ENSP00000379359:Q75E	ENSP00000363822:Q75E	Q	+	1	0	AR	66681936	0.990000	0.36364	0.979000	0.43373	0.394000	0.30568	1.643000	0.37217	1.385000	0.46445	0.495000	0.49567	CAG		TCGA-IB-A5SQ-01A-11D-A32N-08	AR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057007.1	1	0	0	7	86	0	28	0	7.894737e-03	0	2	0	28	2		0	0	0	0	0	2	0	0.877700	0	49	0	18	2	0	0	0	0	0	0		-12.155730	1	0	0	0		1	0	1	1			0.150000	1.900000	0.150000	0.990000	0.460000	1.000000	1.000000	0.888165	0.990000	1	0.700000	1.000000
DACH2	117154	broad.mit.edu	37	X	85969723	85969723	+	Splice_Site	SNP	G	G	T			TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chrX:85969723G>T	ENST00000373125.4	+	6	1104	c.1104G>T	c.(1102-1104)aaG>aaT	p.K368N	DACH2_ENST00000373131.1_Splice_Site_p.K355N|DACH2_ENST00000508860.1_Splice_Site_p.K201N|DACH2_ENST00000510272.1_Splice_Site_p.K149N	NM_053281.3	NP_444511.1	Q96NX9	DACH2_HUMAN	dachshund family transcription factor 2			71					CTGTTATAAAGGTAAGAATCG	0.393000																								0							SO:0001630	splice_region_variant			ENST00000373125.4	1	0	hg19	CCDS14455.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.984771	0.74474	.	.	ENSG00000126733	ENST00000344497;ENST00000373131;ENST00000373125;ENST00000508860;ENST00000510272;ENST00000400297;ENST00000484479	D;D	0.85556	-2.0;-2.0	4.89	4.89	0.63831	.	0.000000	0.64402	D	0.000003	D	0.90841	0.7123	M	0.62723	1.935	0.80722	D	1	D;D;D;D	0.71674	0.996;0.998;0.998;0.993	P;P;D;D	0.71184	0.893;0.883;0.972;0.909	D	0.91059	0.4884	10	0.48119	T	0.1	.	17.3486	0.87316	0.0:0.0:1.0:0.0	.	234;368;355;368	Q1RMF5;A8K3I1;Q96NX9-2;Q96NX9	.;.;.;DACH2_HUMAN	N	368;355;368;201;149;201;23	ENSP00000362223:K355N;ENSP00000362217:K368N	ENSP00000345134:K368N	K	+	3	2	DACH2	85856379	1.000000	0.71417	1.000000	0.80357	0.784000	0.44337	8.894000	0.92506	2.021000	0.59480	0.422000	0.28245	AAG		TCGA-IB-A5SQ-01A-11D-A32N-08	DACH2-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359266.1	1	0	0	34	358	0	66	0	8.096125e-03	0	2	0	66	2		0	0	0	0	0	2	1	1.000000	33	354	0	64	2	0	0	0	0	0	0		-3.075755	1	1	0	0		1	0	1	1			0.150000	1.900000	0.150000	0.990000	0.820000	1.000000	1.000000	0.983155	0.990000	1	0.970000	1.000000
SAMSN1	64092	broad.mit.edu	37	21	15882757	15882757	+	Silent	SNP	A	A	G			TCGA-IB-A5SQ-01A-11D-A32N-08	TCGA-IB-A5SQ-10A-01D-A32N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be12fc83-9cc8-46c6-a210-1fd4e3410bb4	c2c7839f-87cb-4d5f-8089-7b0174efccd9	g.chr21:15882757A>G	ENST00000400566.1	-	5	516	c.435T>C	c.(433-435)ggT>ggC	p.G145G	SAMSN1_ENST00000400564.1_Intron|SAMSN1_ENST00000285670.2_Silent_p.G213G	NM_022136.4	NP_071419.3	Q9NSI8	SAMN1_HUMAN	SAM domain, SH3 domain and nuclear localization signals 1			24					GGTTACTTGTACCATCTGAAC	0.473000																								0							SO:0001819	synonymous_variant			ENST00000400566.1			hg19	CCDS42906.1																																																																																				TCGA-IB-A5SQ-01A-11D-A32N-08	SAMSN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157914.1		0		29	315	0	59	0	5.963782e-01	0	23	0	59	2		0	0	0	0	0	2	1	1.000000	28	314	0	59	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	0	0	0	1.960603	0	0.150000	1.900000	0.122354	0.990000	0.740000	1.000000	1.000000	0.964433	0.990000	1	0.900000	1.000000
