npm - @molgenis/vip-report-template - Versions diffs - 2.7.3 → 3.0.0 - Mend

@molgenis/vip-report-template 2.7.3 → 3.0.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (593) hide show

package/src/mocks/GRCh37/vcf/family.vcf.blob ADDED Viewed

@@ -0,0 +1,104 @@
+##fileformat=VCFv4.2
+##ALT=<ID=DEL,Description="Deletion">
+##ASV_ACMG_class=AnnotSv 'ACMG_class' output.
+##ASV_AnnotSV_ranking_criteria=AnnotSv 'AnnotSV_ranking_criteria' output.
+##ASV_AnnotSV_ranking_score=AnnotSv 'AnnotSV_ranking_score' output.
+##CAPICE_CL=CAPICE classification
+##CAPICE_SC=CAPICE score
+##FILTER=<ID=PASS,Description="All filters passed">
+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=VI,Number=.,Type=String,Description="An enumeration of possible inheritance modes.">
+##FORMAT=<ID=VIC,Number=1,Type=String,Description="Possible Compound hetrozygote variants.">
+##FORMAT=<ID=VID,Number=1,Type=Integer,Description="Inheritance Denovo status.">
+##FORMAT=<ID=VIG,Number=.,Type=String,Description="Genes with an inheritance match.">
+##FORMAT=<ID=VIM,Number=1,Type=Integer,Description="Inheritance Match status.">
+##FORMAT=<ID=VIS,Number=.,Type=String,Description="An enumeration of possible sub inheritance modes like e.g. compound, non penetrance.">
+##HPO=List of HPO terms for the gene
+##INFO=<ID=BND_DEPTH,Number=1,Type=Integer,Description="Read depth at local translocation breakend">
+##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|ALLELE_NUM|DISTANCE|STRAND|FLAGS|PICK|SYMBOL_SOURCE|HGNC_ID|REFSEQ_MATCH|REFSEQ_OFFSET|SOURCE|SIFT|PolyPhen|HGVS_OFFSET|CLIN_SIG|SOMATIC|PHENO|PUBMED|CHECK_REF|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|TRANSCRIPTION_FACTORS|SpliceAI_pred_DP_AG|SpliceAI_pred_DP_AL|SpliceAI_pred_DP_DG|SpliceAI_pred_DP_DL|SpliceAI_pred_DS_AG|SpliceAI_pred_DS_AL|SpliceAI_pred_DS_DG|SpliceAI_pred_DS_DL|SpliceAI_pred_SYMBOL|CAPICE_CL|CAPICE_SC|HPO|IncompletePenetrance|InheritanceModesGene|VKGL_CL|ASV_ACMG_class|ASV_AnnotSV_ranking_criteria|ASV_AnnotSV_ranking_score|gnomAD|gnomAD_AF|gnomAD_HN|VIPC|VIPP|VIPL">
+##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakend">
+##INFO=<ID=MATE_BND_DEPTH,Number=1,Type=Integer,Description="Read depth at remote translocation mate breakend">
+##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
+##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
+##INFO=<ID=gnomAD,Number=.,Type=String,Description="/groups/solve-rd/tmp10/bcharbon/vip/resources/GRCh37/gnomad.total.r2.1.1.sites.stripped.vcf.gz (exact)">
+##INFO=<ID=gnomAD_AF,Number=.,Type=String,Description="AF field from /groups/solve-rd/tmp10/bcharbon/vip/resources/GRCh37/gnomad.total.r2.1.1.sites.stripped.vcf.gz">
+##INFO=<ID=gnomAD_HN,Number=.,Type=String,Description="HN field from /groups/solve-rd/tmp10/bcharbon/vip/resources/GRCh37/gnomad.total.r2.1.1.sites.stripped.vcf.gz">
+##IncompletePenetrance=Boolean indicating if the gene is known for incomplete penetrance.
+##InheritanceModesGene=List of inheritance modes for the gene
+##SpliceAI_pred_DP_AG=SpliceAI predicted effect on splicing. Delta position for acceptor gain
+##SpliceAI_pred_DP_AL=SpliceAI predicted effect on splicing. Delta position for acceptor loss
+##SpliceAI_pred_DP_DG=SpliceAI predicted effect on splicing. Delta position for donor gain
+##SpliceAI_pred_DP_DL=SpliceAI predicted effect on splicing. Delta position for donor loss
+##SpliceAI_pred_DS_AG=SpliceAI predicted effect on splicing. Delta score for acceptor gain
+##SpliceAI_pred_DS_AL=SpliceAI predicted effect on splicing. Delta score for acceptor loss
+##SpliceAI_pred_DS_DG=SpliceAI predicted effect on splicing. Delta score for donor gain
+##SpliceAI_pred_DS_DL=SpliceAI predicted effect on splicing. Delta score for donor loss
+##SpliceAI_pred_SYMBOL=SpliceAI gene symbol
+##VEP="v105" time="2022-06-02 08:49:33" cache="/groups/solve-rd/tmp10/bcharbon/vip/resources/vep/cache/homo_sapiens_refseq/105_GRCh37" ensembl-variation=105.ac8178e ensembl-funcgen=105.660df8f ensembl-io=105.2a0a40c ensembl=105.525fbcb 1000genomes="phase3" COSMIC="92" ClinVar="202012" HGMD-PUBLIC="20204" assembly="GRCh37.p13" dbSNP="154" gencode="GENCODE 19" genebuild="2011-04" gnomAD="r2.1" polyphen="2.2.2" refseq="2020-10-26 17:03:42 - GCF_000001405.25_GRCh37.p13_genomic.gff" regbuild="1.0" sift="sift5.2.2"
+##VIPC=VIP decision tree classification
+##VIPL=VIP decision tree labels (ampersand separated)
+##VIPP=VIP decision tree path (ampersand separated)
+##VIP_Command=nextflow run ./main.nf --input /groups/solve-rd/tmp10/bcharbon/testdata/testdata_b37.vcf --output /groups/solve-rd/tmp10/bcharbon/testdata_out --keep --pedigree /groups/solve-rd/tmp10/bcharbon/example.ped --probands Patient --phenotypes 'HP:0000951;HP:0003124' --assembly GRCh37
+##VIP_Version=4.0.1
+##VIP_treeCommand=--input testdata_b37_chunk0_annotated.vcf.gz --config /groups/solve-rd/tmp10/bcharbon/vip/resources/decision_tree.json --labels 0 --path 0 --output testdata_b37_chunk0_classified.vcf.gz
+##VIP_treeVersion=3.0.0
+##VKGL_CL=VKGL consensus variant classification.
+##contig=<ID=1,length=249250621,assembly=b37>
+##contig=<ID=2,length=243199373,assembly=b37>
+##contig=<ID=3,length=198022430,assembly=b37>
+##contig=<ID=4,length=191154276,assembly=b37>
+##contig=<ID=5,length=180915260,assembly=b37>
+##contig=<ID=6,length=171115067,assembly=b37>
+##contig=<ID=7,length=159138663,assembly=b37>
+##contig=<ID=8,length=146364022,assembly=b37>
+##contig=<ID=9,length=141213431,assembly=b37>
+##contig=<ID=10,length=135534747,assembly=b37>
+##contig=<ID=11,length=135006516,assembly=b37>
+##contig=<ID=12,length=133851895,assembly=b37>
+##contig=<ID=13,length=115169878,assembly=b37>
+##contig=<ID=14,length=107349540,assembly=b37>
+##contig=<ID=15,length=102531392,assembly=b37>
+##contig=<ID=16,length=90354753,assembly=b37>
+##contig=<ID=17,length=81195210,assembly=b37>
+##contig=<ID=18,length=78077248,assembly=b37>
+##contig=<ID=19,length=59128983,assembly=b37>
+##contig=<ID=20,length=63025520,assembly=b37>
+##contig=<ID=21,length=48129895,assembly=b37>
+##contig=<ID=22,length=51304566,assembly=b37>
+##contig=<ID=X,length=155270560,assembly=b37>
+##contig=<ID=Y,length=59373566,assembly=b37>
+##contig=<ID=MT,length=16569,assembly=b37>
+##fileDate=20200320
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Patient	Father	Mother	Sister	Nephew	Unrelated
+1	10042538	.	C	T	.	PASS	CSQ=T|missense_variant|MODERATE|NMNAT1|64802|Transcript|NM_001297778.1|protein_coding|5/5||NM_001297778.1:c.619C>T|NP_001284707.1:p.Arg207Trp|778/3796|619/840|207/279|R/W|Cgg/Tgg|rs142968179&CM127756|1||1||1|EntrezGene|||||0.04|0.08||pathogenic||1&1|26103963&22842229&22842230|||||||0|-36|-16|17|0.00|0.00|0.00|0.00|NMNAT1|VUS|0.16572298|||AR|LP||||1:10042538-10042538|3.88948e-05|0|LP|filter&vkgl&exit_lp|,T|downstream_gene_variant|MODIFIER|NMNAT1|64802|Transcript|NM_001297779.2|protein_coding||||||||||rs142968179&CM127756|1|714|1|||EntrezGene||||||||pathogenic||1&1|26103963&22842229&22842230|||||||0|-36|-16|17|0.00|0.00|0.00|0.00|NMNAT1|VUS|0.033541594|||AR|LP||||1:10042538-10042538|3.88948e-05|0|LP|filter&vkgl&exit_lp|,T|missense_variant|MODERATE|NMNAT1|64802|Transcript|NM_022787.4|protein_coding|5/5||NM_022787.4:c.619C>T|NP_073624.2:p.Arg207Trp|716/3734|619/840|207/279|R/W|Cgg/Tgg|rs142968179&CM127756|1||1|||EntrezGene|||||0.04|0.08||pathogenic||1&1|26103963&22842229&22842230|||||||0|-36|-16|17|0.00|0.00|0.00|0.00|NMNAT1|VUS|0.14321531|||AR|LP||||1:10042538-10042538|3.88948e-05|0|LP|filter&vkgl&exit_lp|	GT:AD:DP:VI:VIC:VID:VIG:VIM	1|1:0,50:50:AR:.:1:64802:1	0|0:50,0:50	0|0:50,0:50	0|0:50,0:50	0|0:50,0:50	0|0:50,0:50
+1	16375583	.	GA	G	.	PASS	CSQ=-|intron_variant|MODIFIER|CLCNKB|1188|Transcript|NM_000085.5|protein_coding||7/19|NM_000085.5:c.656-31del|||||||rs751608665|1||1||1|EntrezGene||||||||uncertain_significance&pathogenic||1||||||||20|45|-14|-45|0.05|0.00|0.00|0.00|CLCNKB|VUS|0.032507|HP:0000951||AR|LP||||1:16375584-16375585|0.000548455|0|LP|filter&vkgl&exit_lp|,-|frameshift_variant|HIGH|CLCNKB|1188|Transcript|NM_001165945.2|protein_coding|1/13||NM_001165945.2:c.118del|NP_001159417.2:p.Arg40GlyfsTer4|328/2174|118/1554|40/517|R/X|Agg/gg|rs751608665|1||1|||EntrezGene||||||||uncertain_significance&pathogenic||1||||||||20|45|-14|-45|0.05|0.00|0.00|0.00|CLCNKB|VUS|0.9770811|HP:0000951||AR|LP||||1:16375584-16375585|0.000548455|0|LP|filter&vkgl&exit_lp|	GT:AD:DP:VI:VIC:VID:VIG:VIM:VIS	1|0:25,25:50:AR:1_16376412_G_A,1_16376412_G_N:0:1188:1:AR_C	1|0:25,25:50	0|0:50,0:50	0|0:50,0:50	0|0:50,0:50	0|0:50,0:50
+1	16376412	n_alt	G	N	.	PASS	CSQ=N|splice_donor_variant|HIGH|CLCNKB|1188|Transcript|NM_000085.5|protein_coding||10/19||||||||CS1211892&CS971662|1||1||1|EntrezGene||||||||||1&1|||||||||||||||||VUS|0.373989|HP:0000951||AR||||||||LP|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_lp|,N|splice_donor_variant|HIGH|CLCNKB|1188|Transcript|NM_001165945.2|protein_coding||3/12||||||||CS1211892&CS971662|1||1|||EntrezGene||||||||||1&1|||||||||||||||||VUS|0.373989|HP:0000951||AR||||||||LP|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_lp|	GT:AD:DP:VI:VIC:VID:VIG:VIM:VIS	1|0:5,45:50:AR,AD:1_16376412_G_A,1_16375583_GA_G:1:1188:1:AR_C	0|0:50,0:50	0|0:50,0:50	0|0:50,0:50	0|0:50,0:50	0|0:50,0:50
+1	16376412	.	G	A	.	PASS	CSQ=A|splice_donor_variant|HIGH|CLCNKB|1188|Transcript|NM_000085.5|protein_coding||10/19|NM_000085.5:c.968+1G>A|||||||rs201204502&CS1211892&CS971662|1||1||1|EntrezGene||||||||||0&1&1||||||||17|-36|-28|-1|0.00|0.00|0.03|0.97|CLCNKB|VUS|0.9855972|HP:0000951||AR|LP||||1:16376412-16376412|6.38086e-05|0|LP|filter&vkgl&exit_lp|,A|splice_donor_variant|HIGH|CLCNKB|1188|Transcript|NM_001165945.2|protein_coding||3/12|NM_001165945.2:c.461+1G>A|||||||rs201204502&CS1211892&CS971662|1||1|||EntrezGene||||||||||0&1&1||||||||17|-36|-28|-1|0.00|0.00|0.03|0.97|CLCNKB|VUS|0.9855972|HP:0000951||AR|LP||||1:16376412-16376412|6.38086e-05|0|LP|filter&vkgl&exit_lp|	GT:AD:DP:VI:VIC:VID:VIG:VIM:VIS	0|1:50:50:AR:1_16375583_GA_G,1_16376412_G_N:0:1188:1:AR_C	0|0:50,0:50	1|0:25,25:50	0|0:50,0:50	0|0:50,0:50	0|0:50,0:50
+1	17349219	g_ref	G	A	.	PASS	CSQ=A|missense_variant|MODERATE|SDHB|6390|Transcript|NM_003000.3|protein_coding|7/8||NM_003000.3:c.649C>T|NP_002991.2:p.Arg217Cys|662/1015|649/843|217/280|R/C|Cgc/Tgc|rs200245469&CM094752&CM1210440&COSV64965760|1||-1||1|EntrezGene|||||0|1||likely_pathogenic|0&0&0&1|1&1&1&1||||||||28|6|6|5|0.00|0.00|0.00|0.00|SDHB|VUS|0.89070946|HP:0000951||AD&AR|LP|||||||LP|filter&vkgl&exit_lp|	GT:AD:DP:VI:VIC:VID:VIG:VIM	1|1:0,50:50:AR:.:1:6390:1	1|0:45,5:50	0|0:50,0:50	1|0:25,25:50	0|0:50,0:50	0|0:50,0:50
+1	17355094	.	C	T	.	PASS	CSQ=T|splice_donor_variant|HIGH|SDHB|6390|Transcript|NM_003000.3|protein_coding||4/7|NM_003000.3:c.423+1G>A|||||||rs398122805&CS056774&CS062098&COSV64965540|1||-1||1|EntrezGene||||||||pathogenic|0&0&0&1|1&1&1&1|21348866&17667967&17804857&16405730&21565294&15383933|||||||-49|12|26|1|0.00|0.00|0.14|0.97|SDHB|VUS|0.9641474|HP:0000951||AD&AR|LP||||1:17355094-17355094|1.19344e-05|0|LP|filter&vkgl&exit_lp|	GT:AD:DP:VI:VIC:VID:VIG:VIM	1|0:5,45:50:AD:.:1:6390:1	0|0:50,0:50	0|0:50,0:50	0|0:50,0:50	0|0:50,0:50	0|0:50,0:50
+1	152520788	symbolic1	A	<DEL>	.	PASS	CSQ=deletion|transcript_ablation|HIGH|LCE3D|84648|Transcript|NM_032563.2|protein_coding|||||||||||1||-1||1|EntrezGene|||||||||||||||||||||||||||||||||||||||LP|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_lp|,deletion|transcript_ablation|HIGH|LCE3E|353145|Transcript|NM_178435.4|protein_coding|||||||||||1||-1|||EntrezGene|||||||||||||||||||||||||||||||||||||||LP|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_lp|,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00701519957||||||||||||1||||||||||||||||||||||||||||||||||||||||||||VUS|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_vus|,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00905971885||||||||||||1||||||||||||||||||||||||||||||||||||||||||||VUS|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_vus|,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00522719201||||||||||||1||||||||||||||||||||||||||||||||||||||||||||VUS|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_vus|;SVLEN=-49314;SVTYPE=DEL	GT:AD:DP:VI:VIC:VID:VIM	1|1:0,50:50:AR:.:1:0	0|0:50,0:50	0|0:50,0:50	0|0:50,0:50	0|0:50,0:50	1|0:25,25:50
+4	106320294	.	G	A	.	PASS	CSQ=A|missense_variant|MODERATE|PPA2|27068|Transcript|NM_006903.4|protein_coding|7/11||NM_006903.4:c.596C>T|NP_008834.3:p.Pro199Leu|616/1586|596/918|199/305|P/L|cCg/cTg|rs138215926&CM1610192&COSV58994362|1||-1|||EntrezGene|||||0|0.985||pathogenic|0&0&1|1&1&1|27523597|||||||-34|27|-2|-43|0.00|0.00|0.00|0.00|PPA2|VUS|0.8097311|||AR|LP||||4:106320294-106320294|0.000211803|0|LP|filter&vkgl&exit_lp|,A|missense_variant|MODERATE|PPA2|27068|Transcript|NM_176866.2|protein_coding|4/8||NM_176866.2:c.377C>T|NP_789842.2:p.Pro126Leu|397/1367|377/699|126/232|P/L|cCg/cTg|rs138215926&CM1610192&COSV58994362|1||-1|||EntrezGene|||||0|0.992||pathogenic|0&0&1|1&1&1|27523597|||||||-34|27|-2|-43|0.00|0.00|0.00|0.00|PPA2|VUS|0.7550335|||AR|LP||||4:106320294-106320294|0.000211803|0|LP|filter&vkgl&exit_lp|,A|missense_variant|MODERATE|PPA2|27068|Transcript|NM_176867.3|protein_coding|2/6||NM_176867.3:c.185C>T|NP_789843.2:p.Pro62Leu|205/1175|185/507|62/168|P/L|cCg/cTg|rs138215926&CM1610192&COSV58994362|1||-1|||EntrezGene|||||0|0.995||pathogenic|0&0&1|1&1&1|27523597|||||||-34|27|-2|-43|0.00|0.00|0.00|0.00|PPA2|VUS|0.8145551|||AR|LP||||4:106320294-106320294|0.000211803|0|LP|filter&vkgl&exit_lp|,A|missense_variant|MODERATE|PPA2|27068|Transcript|NM_176869.3|protein_coding|8/12||NM_176869.3:c.683C>T|NP_789845.1:p.Pro228Leu|695/1665|683/1005|228/334|P/L|cCg/cTg|rs138215926&CM1610192&COSV58994362|1||-1||1|EntrezGene|||||0|0.993||pathogenic|0&0&1|1&1&1|27523597|||||||-34|27|-2|-43|0.00|0.00|0.00|0.00|PPA2|VUS|0.76490384|||AR|LP||||4:106320294-106320294|0.000211803|0|LP|filter&vkgl&exit_lp|,A|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001994744|promoter_flanking_region||||||||||rs138215926&CM1610192&COSV58994362|1|||||||||||||pathogenic|0&0&1|1&1&1|27523597|||||||||||||||||||||||||4:106320294-106320294|0.000211803|0|LP|filter&vkgl&clinVar&exit_lp|	GT:AD:DP:VI:VIC:VID:VIG:VIM	1|1:0,50:50:AR:.:1:27068:1	1|0:25,25:50	0|0:50,0:50	0|0:50,0:50	0|0:50,0:50	1|1:0,50:50
+7	42064957	.	GACTC	G	.	PASS	CSQ=-|frameshift_variant|HIGH|GLI3|2737|Transcript|NM_000168.6|protein_coding|9/15||NM_000168.6:c.1258_1261del|NP_000159.3:p.Glu420LeufsTer3|1539-1542/8405|1258-1261/4743|420-421/1580|ES/X|GAGTct/ct||1||-1||1|EntrezGene||||||||||||||||||18|21|-40|6|0.00|0.00|0.00|0.00|GLI3|VUS|0.9822135||1|AD|LP|||||||LP|filter&vkgl&exit_lp|	GT:AD:DP:VIC:VID:VIM	1|0:25,25:50:.:0:0	1|0:5,45:50	1|1:0,50:50	1|0:25,25:50	0|0:50,0:50	0|0:50,0:50
+8	145140500	.	CAG	C	.	PASS	CSQ=-|frameshift_variant|HIGH|GPAA1|8733|Transcript|NM_003801.4|protein_coding|11/12||NM_003801.4:c.1477_1478del|NP_003792.1:p.Arg493GlyfsTer152|1574-1575/2054|1477-1478/1866|493/621|R/X|AGg/g|rs782339984|1||1||1|EntrezGene||||||||pathogenic||1||||||||-15|-8|12|-21|0.02|0.00|0.00|0.00|GPAA1|VUS|0.99260485|||AR|LP||||8:145140501-145140503|0.000142617|0|LP|filter&vkgl&exit_lp|,-|downstream_gene_variant|MODIFIER|EXOSC4|54512|Transcript|NM_019037.3|protein_coding||||||||||rs782339984|1|4950|1|||EntrezGene||||||||pathogenic||1||||||||-15|-8|12|-21|0.02|0.00|0.00|0.00|GPAA1|VUS|0.14952277||||||||8:145140501-145140503|0.000142617|0|LP|filter&vkgl&clinVar&exit_lp|	GT:AD:DP:VIC:VID:VIM	1|0:25,25:50:.:0:0	1|0:25,25:50	0|0:50,0:50	1|1:0,50:50	0|0:50,0:50	0|0:50,0:50
+9	107546633	.	AAAGAT	A	.	PASS	CSQ=-|frameshift_variant|HIGH|ABCA1|19|Transcript|NM_005502.4|protein_coding|50/50||NM_005502.4:c.6744_6748del|NP_005493.2:p.Phe2250ThrfsTer3|7057-7061/10408|6744-6748/6786|2248-2250/2261|TSF/TX|acATCTTtt/actt||1||-1||1|EntrezGene|||||||||||||||||||||||||||VUS|0.9823047|HP:0000951||AD&AR||||||||LP|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_lp|	GT:AD:DP:VI:VIC:VID:VIG:VIM	1|1:0,10:10:AR:.:0:19:1	0|1:1,49:50	1|0:0,50:50	0|0:50,0:50	0|0:50,0:50	0|0:50,0:50
+9	107584864	.	AC	A	.	PASS	CSQ=-|frameshift_variant|HIGH|ABCA1|19|Transcript|NM_005502.4|protein_coding|19/50||NM_005502.4:c.2740del|NP_005493.2:p.Val914TrpfsTer8|3053/10408|2740/6786|914/2261|V/X|Gtg/tg||1||-1||1|EntrezGene||||||||||||||||||33|-42|28|1|0.00|0.00|0.10|0.00|ABCA1|VUS|0.98804027|HP:0000951||AD&AR|LP|||||||LP|filter&vkgl&exit_lp|	GT:AD:DP:VI:VIC:VID:VIG:VIM	1|0:25,25:50:AD:.:1:19:1	0|0:50,0:50	0|0:50,0:50	0|0:50,0:50	0|0:50,0:50	0|0:50,0:50
+10	126091499	.	G	C	.	PASS	CSQ=C|stop_gained|HIGH|OAT|4942|Transcript|NM_000274.4|protein_coding|7/10||NM_000274.4:c.897C>G|NP_000265.1:p.Tyr299Ter|977/2039|897/1320|299/439|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808|||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.979408|||AR|LP||||10:126091499-126091499|1.59133e-05|0|LP|filter&vkgl&exit_lp|,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001171814.2|protein_coding|6/9||NM_001171814.2:c.483C>G|NP_001165285.1:p.Tyr161Ter|749/1811|483/906|161/301|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808|||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.97846687|||AR|LP||||10:126091499-126091499|1.59133e-05|0|LP|filter&vkgl&exit_lp|,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322965.2|protein_coding|7/10||NM_001322965.2:c.897C>G|NP_001309894.1:p.Tyr299Ter|972/2034|897/1320|299/439|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808|||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.979408|||AR|LP||||10:126091499-126091499|1.59133e-05|0|LP|filter&vkgl&exit_lp|,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322966.2|protein_coding|8/11||NM_001322966.2:c.897C>G|NP_001309895.1:p.Tyr299Ter|1292/2354|897/1320|299/439|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1||1|EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808|||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.9796912|||AR|LP||||10:126091499-126091499|1.59133e-05|0|LP|filter&vkgl&exit_lp|,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322967.2|protein_coding|8/11||NM_001322967.2:c.897C>G|NP_001309896.1:p.Tyr299Ter|1097/2159|897/1320|299/439|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808|||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.9819772|||AR|LP||||10:126091499-126091499|1.59133e-05|0|LP|filter&vkgl&exit_lp|,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322968.2|protein_coding|9/12||NM_001322968.2:c.897C>G|NP_001309897.1:p.Tyr299Ter|1184/2246|897/1320|299/439|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808|||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.9819772|||AR|LP||||10:126091499-126091499|1.59133e-05|0|LP|filter&vkgl&exit_lp|,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322969.2|protein_coding|8/11||NM_001322969.2:c.897C>G|NP_001309898.1:p.Tyr299Ter|1064/2126|897/1320|299/439|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808|||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.9819772|||AR|LP||||10:126091499-126091499|1.59133e-05|0|LP|filter&vkgl&exit_lp|,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322970.2|protein_coding|9/12||NM_001322970.2:c.897C>G|NP_001309899.1:p.Tyr299Ter|1280/2342|897/1320|299/439|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808|||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.9796912|||AR|LP||||10:126091499-126091499|1.59133e-05|0|LP|filter&vkgl&exit_lp|,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322971.2|protein_coding|5/8||NM_001322971.2:c.576C>G|NP_001309900.1:p.Tyr192Ter|656/1718|576/999|192/332|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808|||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.9760591|||AR|LP||||10:126091499-126091499|1.59133e-05|0|LP|filter&vkgl&exit_lp|,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322974.2|protein_coding|7/10||NM_001322974.2:c.297C>G|NP_001309903.1:p.Tyr99Ter|863/1925|297/720|99/239|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808|||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.9775237|||AR|LP||||10:126091499-126091499|1.59133e-05|0|LP|filter&vkgl&exit_lp|	GT:AD:DP:VI:VIC:VID:VIG:VIM	1|1:0,50:50:AR:.:1:4942:1	1|0:25,25:50	0|0:50,0:50	0|0:50,0:50	0|0:50,0:50	0|0:50,0:50
+13	77570128	.	G	A	.	PASS	CSQ=A|missense_variant|MODERATE|CLN5|1203|Transcript|NM_001366624.2|protein_coding|3/5||NM_001366624.2:c.431G>A|NP_001353553.1:p.Cys144Tyr|449/5286|431/594|144/197|C/Y|tGt/tAt|rs1566219136|1||1|||EntrezGene|||||0|0.995||pathogenic||1||||||||-27|-43|-27|-1|0.00|0.00|0.01|0.00|CLN5|VUS|0.79378206|||AR|LP|||||||LP|filter&vkgl&exit_lp|,A|missense_variant|MODERATE|CLN5|1203|Transcript|NM_006493.4|protein_coding|3/4||NM_006493.4:c.431G>A|NP_006484.2:p.Cys144Tyr|449/5243|431/1077|144/358|C/Y|tGt/tAt|rs1566219136|1||1||1|EntrezGene|||||0|0.999||pathogenic||1||||||||-27|-43|-27|-1|0.00|0.00|0.01|0.00|CLN5|VUS|0.862269|||AR|LP|||||||LP|filter&vkgl&exit_lp|	GT:AD:DP:VIC:VID:VIM	1|1:0,50:50:.:1:0	1|1:0,50:50	0|0:50,0:50	0|0:50,0:50	0|0:50,0:50	0|0:50,0:50
+14	89307838	.	C	T	.	PASS	CSQ=T|stop_gained|HIGH|TTC8|123016|Transcript|NM_001288781.1|protein_coding|6/16||NM_001288781.1:c.529C>T|NP_001275710.1:p.Gln177Ter|725/2378|529/1596|177/531|Q/*|Cag/Tag|rs376035653|1||1||1|EntrezGene||||||||||||||||||3|-22|-8|20|0.00|0.00|0.00|0.05|TTC8|VUS|0.9807194|HP:0000951||AR|LP||||14:89307838-89307838|3.99307e-06|0|LP|filter&vkgl&exit_lp|,T|5_prime_UTR_variant|MODIFIER|TTC8|123016|Transcript|NM_001288782.1|protein_coding|6/14||NM_001288782.1:c.-34C>T||725/2298|||||rs376035653|1||1|||EntrezGene||||||||||||||||||3|-22|-8|20|0.00|0.00|0.00|0.05|TTC8|VUS|0.009629895|HP:0000951||AR|LP||||14:89307838-89307838|3.99307e-06|0|LP|filter&vkgl&exit_lp|,T|intron_variant|MODIFIER|TTC8|123016|Transcript|NM_001288783.1|protein_coding||5/14|NM_001288783.1:c.-199+298C>T|||||||rs376035653|1||1|||EntrezGene||||||||||||||||||3|-22|-8|20|0.00|0.00|0.00|0.05|TTC8|VUS|0.0075686513|HP:0000951||AR|LP||||14:89307838-89307838|3.99307e-06|0|LP|filter&vkgl&exit_lp|,T|stop_gained|HIGH|TTC8|123016|Transcript|NM_001366535.2|protein_coding|5/13||NM_001366535.2:c.529C>T|NP_001353464.1:p.Gln177Ter|586/5160|529/1434|177/477|Q/*|Cag/Tag|rs376035653|1||1|||EntrezGene||||||||||||||||||3|-22|-8|20|0.00|0.00|0.00|0.05|TTC8|VUS|0.9817811|HP:0000951||AR|LP||||14:89307838-89307838|3.99307e-06|0|LP|filter&vkgl&exit_lp|,T|intron_variant|MODIFIER|TTC8|123016|Transcript|NM_001366536.2|protein_coding||4/11|NM_001366536.2:c.459+298C>T|||||||rs376035653|1||1|||EntrezGene||||||||||||||||||3|-22|-8|20|0.00|0.00|0.00|0.05|TTC8|VUS|0.0075686513|HP:0000951||AR|LP||||14:89307838-89307838|3.99307e-06|0|LP|filter&vkgl&exit_lp|,T|stop_gained|HIGH|TTC8|123016|Transcript|NM_144596.4|protein_coding|6/15||NM_144596.4:c.559C>T|NP_653197.2:p.Gln187Ter|616/2183|559/1548|187/515|Q/*|Cag/Tag|rs376035653|1||1|||EntrezGene||||||||||||||||||3|-22|-8|20|0.00|0.00|0.00|0.05|TTC8|VUS|0.98182434|HP:0000951||AR|LP||||14:89307838-89307838|3.99307e-06|0|LP|filter&vkgl&exit_lp|,T|stop_gained|HIGH|TTC8|123016|Transcript|NM_198309.3|protein_coding|6/15||NM_198309.3:c.529C>T|NP_938051.1:p.Gln177Ter|725/2300|529/1518|177/505|Q/*|Cag/Tag|rs376035653|1||1|||EntrezGene||||||||||||||||||3|-22|-8|20|0.00|0.00|0.00|0.05|TTC8|VUS|0.9807194|HP:0000951||AR|LP||||14:89307838-89307838|3.99307e-06|0|LP|filter&vkgl&exit_lp|,T|intron_variant|MODIFIER|TTC8|123016|Transcript|NM_198310.3|protein_coding||5/13|NM_198310.3:c.459+298C>T|||||||rs376035653|1||1|||EntrezGene||||||||||||||||||3|-22|-8|20|0.00|0.00|0.00|0.05|TTC8|VUS|0.0075686513|HP:0000951||AR|LP||||14:89307838-89307838|3.99307e-06|0|LP|filter&vkgl&exit_lp|,T|non_coding_transcript_exon_variant|MODIFIER|TTC8|123016|Transcript|NR_159362.2|misc_RNA|5/15||NR_159362.2:n.586C>T||586/5304|||||rs376035653|1||1|||EntrezGene||||||||||||||||||3|-22|-8|20|0.00|0.00|0.00|0.05|TTC8|VUS|0.08789039|HP:0000951||AR|LP||||14:89307838-89307838|3.99307e-06|0|LP|filter&vkgl&exit_lp|	GT:AD:DP:VI:VIC:VID:VIM	1|0:25,25:50:AD:.:1:0	0|0:50,0:50	0|0:50,0:50	0|0:50,0:50	0|0:50,0:50	0|0:50,0:50
+14	89310195	.	G	A	.	PASS	CSQ=A|splice_donor_variant|HIGH|TTC8|123016|Transcript|NM_001288781.1|protein_coding||7/15|NM_001288781.1:c.594+1G>A|||||||rs587777808&CD056477&CS056440|1||1||1|EntrezGene||||||||pathogenic||1&1&1|16308660|||||||32|-45|32|-1|0.00|0.00|0.00|1.00|TTC8|VUS|0.9949398|HP:0000951||AR|LP|||||||LP|filter&vkgl&exit_lp|,A|intron_variant|MODIFIER|TTC8|123016|Transcript|NM_001288782.1|protein_coding||6/13|NM_001288782.1:c.30+2294G>A|||||||rs587777808&CD056477&CS056440|1||1|||EntrezGene||||||||pathogenic||1&1&1|16308660|||||||32|-45|32|-1|0.00|0.00|0.00|1.00|TTC8|VUS|0.19432564|HP:0000951||AR|LP|||||||LP|filter&vkgl&exit_lp|,A|splice_donor_variant|HIGH|TTC8|123016|Transcript|NM_001288783.1|protein_coding||6/14|NM_001288783.1:c.-154+1G>A|||||||rs587777808&CD056477&CS056440|1||1|||EntrezGene||||||||pathogenic||1&1&1|16308660|||||||32|-45|32|-1|0.00|0.00|0.00|1.00|TTC8|VUS|0.9949398|HP:0000951||AR|LP|||||||LP|filter&vkgl&exit_lp|,A|splice_donor_variant|HIGH|TTC8|123016|Transcript|NM_001366535.2|protein_coding||6/12|NM_001366535.2:c.594+1G>A|||||||rs587777808&CD056477&CS056440|1||1|||EntrezGene||||||||pathogenic||1&1&1|16308660|||||||32|-45|32|-1|0.00|0.00|0.00|1.00|TTC8|VUS|0.9949398|HP:0000951||AR|LP|||||||LP|filter&vkgl&exit_lp|,A|splice_donor_variant|HIGH|TTC8|123016|Transcript|NM_001366536.2|protein_coding||5/11|NM_001366536.2:c.504+1G>A|||||||rs587777808&CD056477&CS056440|1||1|||EntrezGene||||||||pathogenic||1&1&1|16308660|||||||32|-45|32|-1|0.00|0.00|0.00|1.00|TTC8|VUS|0.9949398|HP:0000951||AR|LP|||||||LP|filter&vkgl&exit_lp|,A|splice_donor_variant|HIGH|TTC8|123016|Transcript|NM_144596.4|protein_coding||7/14|NM_144596.4:c.624+1G>A|||||||rs587777808&CD056477&CS056440|1||1|||EntrezGene||||||||pathogenic||1&1&1|16308660|||||||32|-45|32|-1|0.00|0.00|0.00|1.00|TTC8|VUS|0.9949398|HP:0000951||AR|LP|||||||LP|filter&vkgl&exit_lp|,A|splice_donor_variant|HIGH|TTC8|123016|Transcript|NM_198309.3|protein_coding||7/14|NM_198309.3:c.594+1G>A|||||||rs587777808&CD056477&CS056440|1||1|||EntrezGene||||||||pathogenic||1&1&1|16308660|||||||32|-45|32|-1|0.00|0.00|0.00|1.00|TTC8|VUS|0.9949398|HP:0000951||AR|LP|||||||LP|filter&vkgl&exit_lp|,A|splice_donor_variant|HIGH|TTC8|123016|Transcript|NM_198310.3|protein_coding||6/13|NM_198310.3:c.504+1G>A|||||||rs587777808&CD056477&CS056440|1||1|||EntrezGene||||||||pathogenic||1&1&1|16308660|||||||32|-45|32|-1|0.00|0.00|0.00|1.00|TTC8|VUS|0.9949398|HP:0000951||AR|LP|||||||LP|filter&vkgl&exit_lp|,A|splice_donor_variant&non_coding_transcript_variant|HIGH|TTC8|123016|Transcript|NR_159362.2|misc_RNA||6/14|NR_159362.2:n.651+1G>A|||||||rs587777808&CD056477&CS056440|1||1|||EntrezGene||||||||pathogenic||1&1&1|16308660|||||||32|-45|32|-1|0.00|0.00|0.00|1.00|TTC8|VUS|0.9951024|HP:0000951||AR|LP|||||||LP|filter&vkgl&exit_lp|	GT:AD:DP:VI:VIC:VID:VIG:VIM	1|1:0,50:50:AR:.:0:123016:1	0|1:.:10	0|1:50:50	0|0:50,0:50	0|0:50,0:50	0|0:50,0:50
+14	89336407	.	TG	T	.	PASS	CSQ=-|frameshift_variant|HIGH|TTC8|123016|Transcript|NM_001288781.1|protein_coding|12/16||NM_001288781.1:c.963del|NP_001275710.1:p.Met321IlefsTer15|1159/2378|963/1596|321/531|M/X|atG/at|rs1431207606|1||1||1|EntrezGene||||||||||||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.9807489|HP:0000951||AR|LP||||14:89336408-89336409|1.19537e-05|0|LP|filter&vkgl&exit_lp|,-|frameshift_variant|HIGH|TTC8|123016|Transcript|NM_001288782.1|protein_coding|10/14||NM_001288782.1:c.321del|NP_001275711.1:p.Met107IlefsTer15|1079/2298|321/954|107/317|M/X|atG/at|rs1431207606|1||1|||EntrezGene||||||||||||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.9838007|HP:0000951||AR|LP||||14:89336408-89336409|1.19537e-05|0|LP|filter&vkgl&exit_lp|,-|frameshift_variant|HIGH|TTC8|123016|Transcript|NM_001288783.1|protein_coding|11/15||NM_001288783.1:c.198del|NP_001275712.1:p.Met66IlefsTer15|1051/2270|198/831|66/276|M/X|atG/at|rs1431207606|1||1|||EntrezGene||||||||||||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.98078203|HP:0000951||AR|LP||||14:89336408-89336409|1.19537e-05|0|LP|filter&vkgl&exit_lp|,-|frameshift_variant|HIGH|TTC8|123016|Transcript|NM_001366535.2|protein_coding|10/13||NM_001366535.2:c.885del|NP_001353464.1:p.Met295IlefsTer15|942/5160|885/1434|295/477|M/X|atG/at|rs1431207606|1||1|||EntrezGene||||||||||||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.9797095|HP:0000951||AR|LP||||14:89336408-89336409|1.19537e-05|0|LP|filter&vkgl&exit_lp|,-|frameshift_variant|HIGH|TTC8|123016|Transcript|NM_001366536.2|protein_coding|9/12||NM_001366536.2:c.795del|NP_001353465.1:p.Met265IlefsTer15|852/5070|795/1344|265/447|M/X|atG/at|rs1431207606|1||1|||EntrezGene||||||||||||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.9856574|HP:0000951||AR|LP||||14:89336408-89336409|1.19537e-05|0|LP|filter&vkgl&exit_lp|,-|frameshift_variant|HIGH|TTC8|123016|Transcript|NM_144596.4|protein_coding|11/15||NM_144596.4:c.915del|NP_653197.2:p.Met305IlefsTer15|972/2183|915/1548|305/515|M/X|atG/at|rs1431207606|1||1|||EntrezGene||||||||||||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.9619866|HP:0000951||AR|LP||||14:89336408-89336409|1.19537e-05|0|LP|filter&vkgl&exit_lp|,-|frameshift_variant|HIGH|TTC8|123016|Transcript|NM_198309.3|protein_coding|11/15||NM_198309.3:c.885del|NP_938051.1:p.Met295IlefsTer15|1081/2300|885/1518|295/505|M/X|atG/at|rs1431207606|1||1|||EntrezGene||||||||||||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.9801349|HP:0000951||AR|LP||||14:89336408-89336409|1.19537e-05|0|LP|filter&vkgl&exit_lp|,-|frameshift_variant|HIGH|TTC8|123016|Transcript|NM_198310.3|protein_coding|10/14||NM_198310.3:c.795del|NP_938052.1:p.Met265IlefsTer15|991/2210|795/1428|265/475|M/X|atG/at|rs1431207606|1||1|||EntrezGene||||||||||||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.9853147|HP:0000951||AR|LP||||14:89336408-89336409|1.19537e-05|0|LP|filter&vkgl&exit_lp|,-|non_coding_transcript_exon_variant|MODIFIER|TTC8|123016|Transcript|NR_159362.2|misc_RNA|11/15||NR_159362.2:n.1002del||1002/5304|||||rs1431207606|1||1|||EntrezGene||||||||||||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.10411882|HP:0000951||AR|LP||||14:89336408-89336409|1.19537e-05|0|LP|filter&vkgl&exit_lp|	GT:AD:DP:VI:VIC:VID:VIG:VIM	1|1:0,50:50:AR:.:1:123016:1	1|0:25,25:50	0|0:50,0:50	0|0:50,0:50	0|0:50,0:50	0|0:50,0:50
+14	105167860	.	T	G	.	PASS	CSQ=G|missense_variant|MODERATE|INF2|64423|Transcript|NM_001031714.4|protein_coding|2/22||NM_001031714.4:c.158T>G|NP_001026884.3:p.Leu53Arg|289/7566|158/3723|53/1240|L/R|cTg/cGg||1||1|||EntrezGene|||||0|0.999||||||||||||-28|-2|37|-2|0.00|0.00|0.00|0.00|INF2|VUS|0.9012849|||AD|LP|||||||LP|filter&vkgl&exit_lp|,G|missense_variant|MODERATE|INF2|64423|Transcript|NM_022489.4|protein_coding|2/23||NM_022489.4:c.158T>G|NP_071934.3:p.Leu53Arg|289/7623|158/3750|53/1249|L/R|cTg/cGg||1||1||1|EntrezGene|||||0|0.999||||||||||||-28|-2|37|-2|0.00|0.00|0.00|0.00|INF2|VUS|0.9012849|||AD|LP|||||||LP|filter&vkgl&exit_lp|,G|missense_variant|MODERATE|INF2|64423|Transcript|NM_032714.3|protein_coding|2/5||NM_032714.3:c.158T>G|NP_116103.1:p.Leu53Arg|289/1692|158/705|53/234|L/R|cTg/cGg||1||1|||EntrezGene|||||0|0.999||||||||||||-28|-2|37|-2|0.00|0.00|0.00|0.00|INF2|VUS|0.9012849|||AD|LP|||||||LP|filter&vkgl&exit_lp|	GT:AD:DP:VI:VIC:VID:VIM	1|1:0,50:50:AR:.:1:0	0|0:50,0:50	1|0:45,5:50	0|0:50,0:50	1|0:25,25:50	0|0:50,0:50
+17	29556064	.	AC	A	.	PASS	CSQ=-|frameshift_variant|HIGH|NF1|4763|Transcript|NM_000267.3|protein_coding|21/57||NM_000267.3:c.2433del|NP_000258.1:p.Ile812LeufsTer9|2816/12362|2433/8457|811/2818|T/X|acC/ac||1||1|||EntrezGene|||||||1|||||||||||-22|-11|12|25|0.00|0.00|0.00|0.00|NF1|VUS|0.9913782|HP:0000951|1|AD|LP|||||||LP|filter&vkgl&exit_lp|,-|frameshift_variant|HIGH|NF1|4763|Transcript|NM_001042492.3|protein_coding|21/58||NM_001042492.3:c.2433del|NP_001035957.1:p.Ile812LeufsTer9|2766/12373|2433/8520|811/2839|T/X|acC/ac||1||1||1|EntrezGene|||||||1|||||||||||-22|-11|12|25|0.00|0.00|0.00|0.00|NF1|VUS|0.9913782|HP:0000951|1|AD|LP|||||||LP|filter&vkgl&exit_lp|	GT:AD:DP:VIC:VID:VIM	1|1:0,50:50:.:1:0	1|1:0,50:50	0|0:50,0:50	1|0:25,25:50	0|0:50,0:50	1|0:25,25:50
+17	29585422	.	A	G	.	PASS	CSQ=G|missense_variant|MODERATE|NF1|4763|Transcript|NM_000267.3|protein_coding|31/57||NM_000267.3:c.4171A>G|NP_000258.1:p.Arg1391Gly|4554/12362|4171/8457|1391/2818|R/G|Aga/Gga|rs1555618515&CM1211610|1||1|||EntrezGene|||||0|0.962||pathogenic||1&1||||||||-48|2|28|-27|0.00|0.00|0.01|0.00|NF1|VUS|0.6458939|HP:0000951|1|AD|LP|||||||LP|filter&vkgl&exit_lp|,G|missense_variant|MODERATE|NF1|4763|Transcript|NM_001042492.3|protein_coding|32/58||NM_001042492.3:c.4234A>G|NP_001035957.1:p.Arg1412Gly|4567/12373|4234/8520|1412/2839|R/G|Aga/Gga|rs1555618515&CM1211610|1||1||1|EntrezGene|||||0|0.988||pathogenic||1&1||||||||-48|2|28|-27|0.00|0.00|0.01|0.00|NF1|VUS|0.7539552|HP:0000951|1|AD|LP|||||||LP|filter&vkgl&exit_lp|	GT:AD:DP:VI:VIC:VID:VIM	1|1:0,50:50:AR:.:1:0	0|1:.:10	0|0:50,0:50	0|0:50,0:50	0|0:50,0:50	0|0:50,0:50
+17	29663879	.	T	G	.	PASS	CSQ=G|missense_variant|MODERATE|NF1|4763|Transcript|NM_000267.3|protein_coding|41/57||NM_000267.3:c.6311T>G|NP_000258.1:p.Leu2104Arg|6694/12362|6311/8457|2104/2818|L/R|cTg/cGg|CM141499&CM143458|1||1|||EntrezGene|||||0|0.994||||1&1||||||||-42|41|-34|8|0.00|0.00|0.00|0.00|NF1|VUS|0.8564539|HP:0000951|1|AD|LP|||||||LP|filter&vkgl&exit_lp|,G|missense_variant|MODERATE|NF1|4763|Transcript|NM_001042492.3|protein_coding|42/58||NM_001042492.3:c.6374T>G|NP_001035957.1:p.Leu2125Arg|6707/12373|6374/8520|2125/2839|L/R|cTg/cGg|CM141499&CM143458|1||1||1|EntrezGene|||||0|0.993||||1&1||||||||-42|41|-34|8|0.00|0.00|0.00|0.00|NF1|VUS|0.8564539|HP:0000951|1|AD|LP|||||||LP|filter&vkgl&exit_lp|	GT:AD:DP:VI:VIC:VID:VIG:VIM:VIS	1|0:25,25:50:AR,AD:17_29683983_C_T:0:4763:1:AD_IP,AR_C	0|0:50,0:50	1|0:25,25:50	0|0:50,0:50	0|0:50,0:50	0|0:50,0:50
+17	29676226	.	T	A	.	PASS	CSQ=A|stop_gained|HIGH|NF1|4763|Transcript|NM_000267.3|protein_coding|48/57||NM_000267.3:c.7215T>A|NP_000258.1:p.Cys2405Ter|7598/12362|7215/8457|2405/2818|C/*|tgT/tgA|rs1567623508&CM143472|1||1|||EntrezGene||||||||pathogenic||1&1||||||||-49|-6|47|43|0.00|0.00|0.00|0.01|NF1|VUS|0.9926594|HP:0000951|1|AD|LP|||||||LP|filter&vkgl&exit_lp|,A|stop_gained|HIGH|NF1|4763|Transcript|NM_001042492.3|protein_coding|49/58||NM_001042492.3:c.7278T>A|NP_001035957.1:p.Cys2426Ter|7611/12373|7278/8520|2426/2839|C/*|tgT/tgA|rs1567623508&CM143472|1||1||1|EntrezGene||||||||pathogenic||1&1||||||||-49|-6|47|43|0.00|0.00|0.00|0.01|NF1|VUS|0.9926594|HP:0000951|1|AD|LP|||||||LP|filter&vkgl&exit_lp|	GT:AD:DP:VI:VIC:VID:VIM	1|1:0,50:50:AR:.:0:0	1|0:25,25:50	0|1:50:50	0|0:50,0:50	0|0:50,0:50	0|0:50,0:50
+17	29683983	.	C	T	.	PASS	CSQ=T|stop_gained|HIGH|NF1|4763|Transcript|NM_000267.3|protein_coding|52/57||NM_000267.3:c.7681C>T|NP_000258.1:p.Gln2561Ter|8064/12362|7681/8457|2561/2818|Q/*|Cag/Tag|CM143479|1||1|||EntrezGene||||||||||1||||||||24|-5|24|36|0.02|0.00|0.00|0.00|NF1|VUS|0.99177766|HP:0000951|1|AD|LP|||||||LP|filter&vkgl&exit_lp|,T|stop_gained|HIGH|NF1|4763|Transcript|NM_001042492.3|protein_coding|53/58||NM_001042492.3:c.7744C>T|NP_001035957.1:p.Gln2582Ter|8077/12373|7744/8520|2582/2839|Q/*|Cag/Tag|CM143479|1||1||1|EntrezGene||||||||||1||||||||24|-5|24|36|0.02|0.00|0.00|0.00|NF1|VUS|0.9919058|HP:0000951|1|AD|LP|||||||LP|filter&vkgl&exit_lp|	GT:AD:DP:VI:VIC:VID:VIG:VIM:VIS	1|0:25,25:50:AR,AD:17_29663879_T_G:1:4763:1:AR_C	0|0:50,0:50	0|0:50,0:50	0|0:50,0:50	0|0:50,0:50	0|0:50,0:50
+19	11216146	.	C	G	.	PASS	CSQ=G|stop_gained|HIGH|LDLR|3949|Transcript|NM_000527.5|protein_coding|4/18||NM_000527.5:c.564C>G|NP_000518.1:p.Tyr188Ter|650/5173|564/2583|188/860|Y/*|taC/taG|rs121908034&CM920416&COSV99370340|1||1||1|EntrezGene||||||||pathogenic/likely_pathogenic&pathogenic|0&0&1|1&1&1|25741868&27765764&17142622&8882879&1734722&10422803|||||||1|11|0|-14|0.00|0.00|0.00|0.00|LDLR|VUS|0.97590667|HP:0000951&HP:0003124||AD&AR|LP|||||||LP|filter&vkgl&exit_lp|,G|stop_gained|HIGH|LDLR|3949|Transcript|NM_001195798.2|protein_coding|4/18||NM_001195798.2:c.564C>G|NP_001182727.1:p.Tyr188Ter|650/5167|564/2577|188/858|Y/*|taC/taG|rs121908034&CM920416&COSV99370340|1||1|||EntrezGene||||||||pathogenic/likely_pathogenic&pathogenic|0&0&1|1&1&1|25741868&27765764&17142622&8882879&1734722&10422803|||||||1|11|0|-14|0.00|0.00|0.00|0.00|LDLR|VUS|0.97590667|HP:0000951&HP:0003124||AD&AR|LP|||||||LP|filter&vkgl&exit_lp|,G|stop_gained|HIGH|LDLR|3949|Transcript|NM_001195799.2|protein_coding|3/17||NM_001195799.2:c.441C>G|NP_001182728.1:p.Tyr147Ter|527/5050|441/2460|147/819|Y/*|taC/taG|rs121908034&CM920416&COSV99370340|1||1|||EntrezGene||||||||pathogenic/likely_pathogenic&pathogenic|0&0&1|1&1&1|25741868&27765764&17142622&8882879&1734722&10422803|||||||1|11|0|-14|0.00|0.00|0.00|0.00|LDLR|VUS|0.9765647|HP:0000951&HP:0003124||AD&AR|LP|||||||LP|filter&vkgl&exit_lp|,G|intron_variant|MODIFIER|LDLR|3949|Transcript|NM_001195800.2|protein_coding||3/15|NM_001195800.2:c.314-1922C>G|||||||rs121908034&CM920416&COSV99370340|1||1|||EntrezGene||||||||pathogenic/likely_pathogenic&pathogenic|0&0&1|1&1&1|25741868&27765764&17142622&8882879&1734722&10422803|||||||1|11|0|-14|0.00|0.00|0.00|0.00|LDLR|VUS|0.0055715204|HP:0000951&HP:0003124||AD&AR|LP|||||||LP|filter&vkgl&exit_lp|,G|intron_variant|MODIFIER|LDLR|3949|Transcript|NM_001195803.2|protein_coding||3/15|NM_001195803.2:c.314-1095C>G|||||||rs121908034&CM920416&COSV99370340|1||1|||EntrezGene||||||||pathogenic/likely_pathogenic&pathogenic|0&0&1|1&1&1|25741868&27765764&17142622&8882879&1734722&10422803|||||||1|11|0|-14|0.00|0.00|0.00|0.00|LDLR|VUS|0.0055715204|HP:0000951&HP:0003124||AD&AR|LP|||||||LP|filter&vkgl&exit_lp|	GT:AD:DP:VIC:VID:VIM	1|0:5,5:10:.:0:0	1|0:25,25:50	1|0:25,25:50	0|0:50,0:50	0|0:50,0:50	0|0:50,0:50
+19	11224051	.	C	CGTGGTCGCTCTGGACACGGAG	.	PASS	CSQ=TCGCTCTGGACACGGAGGTGG|inframe_insertion|MODERATE|LDLR|3949|Transcript|NM_000527.5|protein_coding|9/18||NM_000527.5:c.1289_1309dup|NP_000518.1:p.Val430_Val436dup|1395-1396/5173|1309-1310/2583|437/860|A/VALDTEVA|gcc/gTCGCTCTGGACACGGAGGTGGcc||1||1||1|EntrezGene|||||||25||||||||||||||||||||VUS|0.27201134|HP:0000951&HP:0003124||AD&AR|LP|||||||LP|filter&vkgl&exit_lp|,TCGCTCTGGACACGGAGGTGG|inframe_insertion|MODERATE|LDLR|3949|Transcript|NM_001195798.2|protein_coding|9/18||NM_001195798.2:c.1289_1309dup|NP_001182727.1:p.Val430_Val436dup|1395-1396/5167|1309-1310/2577|437/858|A/VALDTEVA|gcc/gTCGCTCTGGACACGGAGGTGGcc||1||1|||EntrezGene|||||||25||||||||||||||||||||VUS|0.27201134|HP:0000951&HP:0003124||AD&AR|LP|||||||LP|filter&vkgl&exit_lp|,TCGCTCTGGACACGGAGGTGG|inframe_insertion|MODERATE|LDLR|3949|Transcript|NM_001195799.2|protein_coding|8/17||NM_001195799.2:c.1166_1186dup|NP_001182728.1:p.Val389_Val395dup|1272-1273/5050|1186-1187/2460|396/819|A/VALDTEVA|gcc/gTCGCTCTGGACACGGAGGTGGcc||1||1|||EntrezGene|||||||25||||||||||||||||||||VUS|0.26963568|HP:0000951&HP:0003124||AD&AR|LP|||||||LP|filter&vkgl&exit_lp|,TCGCTCTGGACACGGAGGTGG|inframe_insertion|MODERATE|LDLR|3949|Transcript|NM_001195800.2|protein_coding|7/16||NM_001195800.2:c.785_805dup|NP_001182729.1:p.Val262_Val268dup|891-892/4669|805-806/2079|269/692|A/VALDTEVA|gcc/gTCGCTCTGGACACGGAGGTGGcc||1||1|||EntrezGene|||||||25||||||||||||||||||||VUS|0.3952981|HP:0000951&HP:0003124||AD&AR|LP|||||||LP|filter&vkgl&exit_lp|,TCGCTCTGGACACGGAGGTGG|inframe_insertion|MODERATE|LDLR|3949|Transcript|NM_001195803.2|protein_coding|8/16||NM_001195803.2:c.908_928dup|NP_001182732.1:p.Val303_Val309dup|1014-1015/4639|928-929/2049|310/682|A/VALDTEVA|gcc/gTCGCTCTGGACACGGAGGTGGcc||1||1|||EntrezGene|||||||25||||||||||||||||||||VUS|0.30903387|HP:0000951&HP:0003124||AD&AR|LP|||||||LP|filter&vkgl&exit_lp|	GT:AD:DP:VI:VIC:VID:VIG:VIM	1|1:.:10:AR:.:0:3949:1	0|1:.:10	1|0:25,25:50	0|0:50,0:50	0|0:50,0:50	0|0:50,0:50
+19	17449399	.	C	T	.	PASS	CSQ=T|missense_variant|MODERATE|GTPBP3|84705|Transcript|NM_001128855.3|protein_coding|4/9||NM_001128855.3:c.440C>T|NP_001122327.1:p.Ala147Val|499/2503|440/1416|147/471|A/V|gCg/gTg|rs774708853&COSV50176281|1||1|||EntrezGene|||||0|0.999||likely_pathogenic|0&1|1&1||||||||-39|-47|-19|31|0.01|0.00|0.00|0.00|GTPBP3|VUS|0.8068815|HP:0000951||AR|LP||||19:17449399-17449399|7.96883e-06|0|LP|filter&vkgl&exit_lp|,T|missense_variant|MODERATE|GTPBP3|84705|Transcript|NM_001195422.1|protein_coding|4/9||NM_001195422.1:c.506C>T|NP_001182351.1:p.Ala169Val|528/2595|506/1545|169/514|A/V|gCg/gTg|rs774708853&COSV50176281|1||1|||EntrezGene|||||0|0.997||likely_pathogenic|0&1|1&1||||||||-39|-47|-19|31|0.01|0.00|0.00|0.00|GTPBP3|VUS|0.75153595|HP:0000951||AR|LP||||19:17449399-17449399|7.96883e-06|0|LP|filter&vkgl&exit_lp|,T|upstream_gene_variant|MODIFIER|ANO8|57719|Transcript|NM_020959.3|protein_coding||||||||||rs774708853&COSV50176281|1|3735|-1|||EntrezGene||||||||likely_pathogenic|0&1|1&1||||||||-39|-47|-19|31|0.01|0.00|0.00|0.00|GTPBP3|VUS|0.0217757||||||||19:17449399-17449399|7.96883e-06|0|LP|filter&vkgl&clinVar&exit_lp|,T|missense_variant|MODERATE|GTPBP3|84705|Transcript|NM_032620.4|protein_coding|4/9||NM_032620.4:c.440C>T|NP_116009.2:p.Ala147Val|499/2566|440/1479|147/492|A/V|gCg/gTg|rs774708853&COSV50176281|1||1|||EntrezGene|||||0|0.999||likely_pathogenic|0&1|1&1||||||||-39|-47|-19|31|0.01|0.00|0.00|0.00|GTPBP3|VUS|0.8068815|HP:0000951||AR|LP||||19:17449399-17449399|7.96883e-06|0|LP|filter&vkgl&exit_lp|,T|missense_variant|MODERATE|GTPBP3|84705|Transcript|NM_133644.4|protein_coding|4/8||NM_133644.4:c.440C>T|NP_598399.2:p.Ala147Val|499/2662|440/1575|147/524|A/V|gCg/gTg|rs774708853&COSV50176281|1||1||1|EntrezGene|||||0|0.999||likely_pathogenic|0&1|1&1||||||||-39|-47|-19|31|0.01|0.00|0.00|0.00|GTPBP3|VUS|0.8068815|HP:0000951||AR|LP||||19:17449399-17449399|7.96883e-06|0|LP|filter&vkgl&exit_lp|,T|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000107883|promoter||||||||||rs774708853&COSV50176281|1|||||||||||||likely_pathogenic|0&1|1&1||||||||||||||||||||||||||19:17449399-17449399|7.96883e-06|0|LP|filter&vkgl&clinVar&exit_lp|	GT:AD:DP:VI:VIC:VID:VIM	1|0:25,25:50:AD:.:1:0	0|0:50,0:50	0|0:50,0:50	0|0:50,0:50	0|0:50,0:50	0|0:50,0:50
+19	17451997	.	GA	G	.	PASS	CSQ=-|frameshift_variant|HIGH|GTPBP3|84705|Transcript|NM_001128855.3|protein_coding|8/9||NM_001128855.3:c.1058del|NP_001122327.1:p.Asn353ThrfsTer26|1117/2503|1058/1416|353/471|N/X|aAc/ac||1||1|||EntrezGene|||||||1|||||||||||34|33|-7|33|0.01|0.00|0.00|0.00|GTPBP3|VUS|0.9804278|HP:0000951||AR|LP|||||||LP|filter&vkgl&exit_lp|,-|frameshift_variant|HIGH|GTPBP3|84705|Transcript|NM_001195422.1|protein_coding|8/9||NM_001195422.1:c.1187del|NP_001182351.1:p.Asn396ThrfsTer26|1209/2595|1187/1545|396/514|N/X|aAc/ac||1||1|||EntrezGene|||||||1|||||||||||34|33|-7|33|0.01|0.00|0.00|0.00|GTPBP3|VUS|0.98119754|HP:0000951||AR|LP|||||||LP|filter&vkgl&exit_lp|,-|frameshift_variant|HIGH|GTPBP3|84705|Transcript|NM_032620.4|protein_coding|8/9||NM_032620.4:c.1121del|NP_116009.2:p.Asn374ThrfsTer26|1180/2566|1121/1479|374/492|N/X|aAc/ac||1||1|||EntrezGene|||||||1|||||||||||34|33|-7|33|0.01|0.00|0.00|0.00|GTPBP3|VUS|0.98185974|HP:0000951||AR|LP|||||||LP|filter&vkgl&exit_lp|,-|frameshift_variant|HIGH|GTPBP3|84705|Transcript|NM_133644.4|protein_coding|7/8||NM_133644.4:c.1217del|NP_598399.2:p.Asn406ThrfsTer26|1276/2662|1217/1575|406/524|N/X|aAc/ac||1||1||1|EntrezGene|||||||1|||||||||||34|33|-7|33|0.01|0.00|0.00|0.00|GTPBP3|VUS|0.97986597|HP:0000951||AR|LP|||||||LP|filter&vkgl&exit_lp|	GT:AD:DP:VIC:VID:VIM	1|1:0,50:50:.:1:0	0|0:10,0:10	0|0:50,0:50	1|0:25,25:50	1|1:0,50:50	1|1:0,50:50
+22	50721546	.	C	T	.	PASS	CSQ=T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376864.1|protein_coding|17/37||NM_001376864.1:c.2749G>A|NP_001363793.1:p.Gly917Ser|2881/6611|2749/5754|917/1917|G/S|Ggc/Agc|rs1377653283|1||-1||1|EntrezGene||||||||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.14842245||||||||22:50721546-50721546|4.49665e-06|0|VUS|filter&vkgl&clinVar&gnomad&effect&sift&polyphen&impact&exit_vus|,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376865.1|protein_coding|18/38||NM_001376865.1:c.2818G>A|NP_001363794.1:p.Gly940Ser|2898/6391|2818/5586|940/1861|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene||||||||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.14842245||||||||22:50721546-50721546|4.49665e-06|0|VUS|filter&vkgl&clinVar&gnomad&effect&sift&polyphen&impact&exit_vus|,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376866.1|protein_coding|17/37||NM_001376866.1:c.2749G>A|NP_001363795.1:p.Gly917Ser|2909/6402|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.92206705||||||||22:50721546-50721546|4.49665e-06|0|LP|filter&vkgl&clinVar&gnomad&effect&sift&exit_lp|,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376867.1|protein_coding|18/38||NM_001376867.1:c.2749G>A|NP_001363796.1:p.Gly917Ser|2969/6462|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.92206705||||||||22:50721546-50721546|4.49665e-06|0|LP|filter&vkgl&clinVar&gnomad&effect&sift&exit_lp|,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376868.1|protein_coding|18/38||NM_001376868.1:c.2749G>A|NP_001363797.1:p.Gly917Ser|2962/6455|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.92206705||||||||22:50721546-50721546|4.49665e-06|0|LP|filter&vkgl&clinVar&gnomad&effect&sift&exit_lp|,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376869.1|protein_coding|16/36||NM_001376869.1:c.2749G>A|NP_001363798.1:p.Gly917Ser|2856/6349|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.92206705||||||||22:50721546-50721546|4.49665e-06|0|LP|filter&vkgl&clinVar&gnomad&effect&sift&exit_lp|,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376870.1|protein_coding|17/37||NM_001376870.1:c.2749G>A|NP_001363799.1:p.Gly917Ser|2881/6374|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.92206705||||||||22:50721546-50721546|4.49665e-06|0|LP|filter&vkgl&clinVar&gnomad&effect&sift&exit_lp|,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376871.1|protein_coding|17/37||NM_001376871.1:c.2749G>A|NP_001363800.1:p.Gly917Ser|2874/6367|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.92206705||||||||22:50721546-50721546|4.49665e-06|0|LP|filter&vkgl&clinVar&gnomad&effect&sift&exit_lp|,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376872.1|protein_coding|19/39||NM_001376872.1:c.2749G>A|NP_001363801.1:p.Gly917Ser|3066/6559|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.92206705||||||||22:50721546-50721546|4.49665e-06|0|LP|filter&vkgl&clinVar&gnomad&effect&sift&exit_lp|,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376873.1|protein_coding|18/38||NM_001376873.1:c.2749G>A|NP_001363802.1:p.Gly917Ser|3218/6711|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.92206705||||||||22:50721546-50721546|4.49665e-06|0|LP|filter&vkgl&clinVar&gnomad&effect&sift&exit_lp|,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376874.1|protein_coding|18/38||NM_001376874.1:c.2749G>A|NP_001363803.1:p.Gly917Ser|2934/6427|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.92206705||||||||22:50721546-50721546|4.49665e-06|0|LP|filter&vkgl&clinVar&gnomad&effect&sift&exit_lp|,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376875.1|protein_coding|16/36||NM_001376875.1:c.2749G>A|NP_001363804.1:p.Gly917Ser|2933/6426|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.92206705||||||||22:50721546-50721546|4.49665e-06|0|LP|filter&vkgl&clinVar&gnomad&effect&sift&exit_lp|,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376876.1|protein_coding|18/38||NM_001376876.1:c.2749G>A|NP_001363805.1:p.Gly917Ser|2927/6420|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.92206705||||||||22:50721546-50721546|4.49665e-06|0|LP|filter&vkgl&clinVar&gnomad&effect&sift&exit_lp|,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376877.1|protein_coding|18/38||NM_001376877.1:c.2749G>A|NP_001363806.1:p.Gly917Ser|3198/6691|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.92206705||||||||22:50721546-50721546|4.49665e-06|0|LP|filter&vkgl&clinVar&gnomad&effect&sift&exit_lp|,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376878.1|protein_coding|16/36||NM_001376878.1:c.2749G>A|NP_001363807.1:p.Gly917Ser|2821/6314|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.92206705||||||||22:50721546-50721546|4.49665e-06|0|LP|filter&vkgl&clinVar&gnomad&effect&sift&exit_lp|,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376879.1|protein_coding|19/39||NM_001376879.1:c.2749G>A|NP_001363808.1:p.Gly917Ser|3101/6594|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.92206705||||||||22:50721546-50721546|4.49665e-06|0|LP|filter&vkgl&clinVar&gnomad&effect&sift&exit_lp|,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376880.1|protein_coding|17/37||NM_001376880.1:c.2749G>A|NP_001363809.1:p.Gly917Ser|2991/6484|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.92206705||||||||22:50721546-50721546|4.49665e-06|0|LP|filter&vkgl&clinVar&gnomad&effect&sift&exit_lp|,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376881.1|protein_coding|18/38||NM_001376881.1:c.2749G>A|NP_001363810.1:p.Gly917Ser|3046/6539|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.92206705||||||||22:50721546-50721546|4.49665e-06|0|LP|filter&vkgl&clinVar&gnomad&effect&sift&exit_lp|,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376882.1|protein_coding|17/37||NM_001376882.1:c.2749G>A|NP_001363811.1:p.Gly917Ser|3165/6658|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.92206705||||||||22:50721546-50721546|4.49665e-06|0|LP|filter&vkgl&clinVar&gnomad&effect&sift&exit_lp|,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376883.1|protein_coding|17/37||NM_001376883.1:c.2749G>A|NP_001363812.1:p.Gly917Ser|2881/6350|2749/5493|917/1830|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene||||||||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.14842245||||||||22:50721546-50721546|4.49665e-06|0|VUS|filter&vkgl&clinVar&gnomad&effect&sift&polyphen&impact&exit_vus|,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376884.1|protein_coding|16/36||NM_001376884.1:c.2749G>A|NP_001363813.1:p.Gly917Ser|2821/6236|2749/5439|917/1812|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene||||||||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.14842245||||||||22:50721546-50721546|4.49665e-06|0|VUS|filter&vkgl&clinVar&gnomad&effect&sift&polyphen&impact&exit_vus|,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376885.1|protein_coding|17/37||NM_001376885.1:c.2749G>A|NP_001363814.1:p.Gly917Ser|2909/6324|2749/5439|917/1812|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene||||||||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.14842245||||||||22:50721546-50721546|4.49665e-06|0|VUS|filter&vkgl&clinVar&gnomad&effect&sift&polyphen&impact&exit_vus|,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376886.1|protein_coding|17/37||NM_001376886.1:c.2656G>A|NP_001363815.1:p.Gly886Ser|2876/6369|2656/5424|886/1807|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene||||||||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.14842245||||||||22:50721546-50721546|4.49665e-06|0|VUS|filter&vkgl&clinVar&gnomad&effect&sift&polyphen&impact&exit_vus|,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_012401.4|protein_coding|17/37||NM_012401.4:c.2749G>A|NP_036533.2:p.Gly917Ser|2916/6409|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.92206705||||||||22:50721546-50721546|4.49665e-06|0|LP|filter&vkgl&clinVar&gnomad&effect&sift&exit_lp|	GT:AD:DP:VI:VIC:VID:VIM	1|1:0,50:50:AR:.:1:0	0|0:10,0:10	1|0:25,25:50	0|0:50,0:50	1|0:25,25:50	0|0:50,0:50
+X	48933021	x_chrom	A	T	.	PASS	CSQ=T|splice_donor_variant|HIGH|WDR45|11152|Transcript|NM_001029896.2|protein_coding||9/10|NM_001029896.2:c.827+2T>A|||||||CS135341|1||-1|||EntrezGene||||||||||1||||||||27|28|-2|2|0.02|0.00|0.01|0.99|WDR45|VUS|0.9700852|HP:0000951||XL|LP|||||||LP|filter&vkgl&exit_lp|,T|splice_donor_variant|HIGH|WDR45|11152|Transcript|NM_007075.4|protein_coding||10/11|NM_007075.4:c.830+2T>A|||||||CS135341|1||-1||1|EntrezGene||||||||||1||||||||27|28|-2|2|0.02|0.00|0.01|0.99|WDR45|VUS|0.9700852|HP:0000951||XL|LP|||||||LP|filter&vkgl&exit_lp|,T|upstream_gene_variant|MODIFIER|PRAF2|11230|Transcript|NM_007213.3|protein_coding||||||||||CS135341|1|1360|-1|||EntrezGene||||||||||1||||||||27|28|-2|2|0.02|0.00|0.01|0.99|WDR45|VUS|0.0149048455|||||||||||LP|filter&vkgl&clinVar&gnomad&effect&spliceAI&exit_lp|	GT:AD:DP:VIC:VID:VIM	1|0:25,25:50:.:1:0	1|0:25,25:50	0|0:50,0:50	1|1:0,50:50	0|0:50,0:50	1|1:0,50:50
+Y	2655641	y_chrom	G	A	.	PASS	CSQ=A|stop_gained|HIGH|SRY|6736|Transcript|NM_003140.3|protein_coding|1/1||NM_003140.3:c.4C>T|NP_003131.1:p.Gln2Ter|83/828|4/615|2/204|Q/*|Caa/Taa|rs104894977&CM981858|1||-1||1|EntrezGene||||||||pathogenic||1&1|2401216&9443877|||||||-26|-50|2|-4|0.01|0.00|0.00|0.00|SRY|VUS|0.8890525|||||||||||LP|filter&vkgl&clinVar&exit_lp|	GT:AD:DP:VIC:VID:VIM	1:50:50:.:1:0	0:.:10	.	.	1:50:50	1:50:50

package/src/mocks/GRCh37/vcf/no_vep.vcf.blob ADDED Viewed

@@ -0,0 +1,61 @@
+##fileformat=VCFv4.3
+##fileDate=20200320
+##contig=<ID=1,length=249250621,assembly=b37>
+##contig=<ID=2,length=243199373,assembly=b37>
+##contig=<ID=3,length=198022430,assembly=b37>
+##contig=<ID=4,length=191154276,assembly=b37>
+##contig=<ID=5,length=180915260,assembly=b37>
+##contig=<ID=6,length=171115067,assembly=b37>
+##contig=<ID=7,length=159138663,assembly=b37>
+##contig=<ID=8,length=146364022,assembly=b37>
+##contig=<ID=9,length=141213431,assembly=b37>
+##contig=<ID=10,length=135534747,assembly=b37>
+##contig=<ID=11,length=135006516,assembly=b37>
+##contig=<ID=12,length=133851895,assembly=b37>
+##contig=<ID=13,length=115169878,assembly=b37>
+##contig=<ID=14,length=107349540,assembly=b37>
+##contig=<ID=15,length=102531392,assembly=b37>
+##contig=<ID=16,length=90354753,assembly=b37>
+##contig=<ID=17,length=81195210,assembly=b37>
+##contig=<ID=18,length=78077248,assembly=b37>
+##contig=<ID=19,length=59128983,assembly=b37>
+##contig=<ID=20,length=63025520,assembly=b37>
+##contig=<ID=21,length=48129895,assembly=b37>
+##contig=<ID=22,length=51304566,assembly=b37>
+##contig=<ID=X,length=155270560,assembly=b37>
+##contig=<ID=Y,length=59373566,assembly=b37>
+##contig=<ID=MT,length=16569,assembly=b37>
+##ALT=<ID=DEL,Description="Deletion">
+##ALT=<ID=INS,Description="Insertion">
+##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
+##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
+##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakend">
+##INFO=<ID=BND_DEPTH,Number=1,Type=Integer,Description="Read depth at local translocation breakend">
+##INFO=<ID=MATE_BND_DEPTH,Number=1,Type=Integer,Description="Read depth at remote translocation mate breakend">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Patient	Father	Mother	Sister	Nephew	Unrelated
+1	10042538	.	C	T	.	PASS	.	GT:DP	1|0:50	0|0:10	0|0:50	0|0:50	0|0:50	0|0:50
+1	152520788	symbolic1	A	<DEL>	.	PASS	SVLEN=-49314;SVTYPE=DEL	GT:DP	1|0:50	0|0:10	0|0:50	0|0:50	0|0:50	0|0:50
+2	47635667	symbolic2	G	<INS>	.	PASS	SVLEN=-49314;SVTYPE=INS	GT:DP	1|0:50	0|0:10	0|0:50	0|0:50	0|0:50	0|0:50
+4	106320294	.	G	A	.	PASS	.	GT:DP	1|0:50	0|0:10	0|0:50	0|0:50	0|0:50	0|0:50
+7	42017311	single_breakend_nation	C	C.	.	PASS	SVTYPE=BND	GT:DP	1|0:50	0|0:10	0|0:50	0|0:50	0|0:50	0|0:50
+7	42064957	.	GACTC	G	.	PASS	.	GT:DP	1|0:50	0|0:10	0|0:50	0|0:50	0|0:50	0|0:50
+8	61765143	breakend1	G	]11:134014225]G	.	PASS	SVTYPE=BND;MATEID=breakend2;BND_DEPTH=26;MATE_BND_DEPTH=39	GT:DP	1|0:50	0|0:10	0|0:50	0|0:50	0|0:50	0|0:50
+8	145140500	.	CAG	C	.	PASS	.	GT:DP	1|0:50	0|0:10	0|0:50	0|0:50	0|0:50	0|0:50
+9	107546633	.	AAAGAT	A	.	PASS	.	GT:DP	1|0:50	0|0:10	0|0:50	0|0:50	0|0:50	0|0:50
+10	126091499	.	G	C	.	PASS	.	GT:DP	1|0:50	0|0:10	0|0:50	0|0:50	0|0:50	0|0:50
+11	134014225	breakend2	G	G[8:61765143[	.	PASS	SVTYPE=BND;MATEID=breakend1;BND_DEPTH=39;MATE_BND_DEPTH=26	GT:DP	1|0:50	0|0:10	0|0:50	0|0:50	0|0:50	0|0:50
+13	77570128	.	G	A	.	PASS	.	GT:DP	1|0:50	0|0:10	0|0:50	0|0:50	0|0:50	0|0:50
+14	89336407	.	TG	T	.	PASS	.	GT:DP	1|0:50	0|0:10	0|0:50	0|0:50	0|0:50	0|0:50
+14	105167860	.	T	G	.	PASS	.	GT:DP	1|0:50	0|0:10	0|0:50	0|0:50	0|0:50	0|0:50
+17	29556064	.	AC	A	.	PASS	.	GT:DP	1|0:50	0|0:10	0|0:50	0|0:50	0|0:50	0|0:50
+17	29663879	.	T	G	.	PASS	.	GT:DP	1|0:50	0|0:10	0|0:50	0|0:50	0|0:50	0|0:50
+19	11216146	.	C	G	.	PASS	.	GT:DP	1|0:50	0|0:10	0|0:50	0|0:50	0|0:50	0|0:50
+19	17451997	.	GA	G	.	PASS	.	GT:DP	1|0:50	0|0:10	0|0:50	0|0:50	0|0:50	0|0:50
+20	62326992	.	C	T	.	PASS	.	GT:DP	1|0:50	0|0:10	0|0:50	0|0:50	0|0:50	0|0:50
+22	50627593	.	C	CTG	.	.	.	GT:DP	1|0:50	0|0:10	0|0:50	0|0:50	0|0:50	0|0:50
+22	50721546	.	C	T	.	PASS	.	GT:DP	1|0:50	0|0:10	0|0:50	0|0:50	0|0:50	0|0:50
+X	48933021	x_chrom	A	T	.	PASS	.	GT:DP	1|0:50	0|0:10	0|0:50	0|0:50	0|0:50	0|0:50
+Y	2655641	y_chrom	G	A	.	PASS	.	GT:DP	1:50	0:10	.	.	1:50	1:50
+MT	15326	mt_chrom	A	G	.	PASS	.	GT:DP	1|0:50	0|0:10	0|0:50	0|0:50	0|0:50	0|0:50

package/src/mocks/GRCh37/vcf/samples_0.vcf.blob ADDED Viewed

@@ -0,0 +1,93 @@
+##fileformat=VCFv4.2
+##ALT=<ID=DEL,Description="Deletion">
+##ASV_ACMG_class=AnnotSv 'ACMG_class' output.
+##ASV_AnnotSV_ranking_criteria=AnnotSv 'AnnotSV_ranking_criteria' output.
+##ASV_AnnotSV_ranking_score=AnnotSv 'AnnotSV_ranking_score' output.
+##CAPICE_CL=CAPICE classification
+##CAPICE_SC=CAPICE score
+##FILTER=<ID=PASS,Description="All filters passed">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##HPO=List of HPO terms for the gene
+##INFO=<ID=BND_DEPTH,Number=1,Type=Integer,Description="Read depth at local translocation breakend">
+##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|ALLELE_NUM|DISTANCE|STRAND|FLAGS|PICK|SYMBOL_SOURCE|HGNC_ID|REFSEQ_MATCH|REFSEQ_OFFSET|SOURCE|SIFT|PolyPhen|HGVS_OFFSET|CLIN_SIG|SOMATIC|PHENO|PUBMED|CHECK_REF|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|TRANSCRIPTION_FACTORS|SpliceAI_pred_DP_AG|SpliceAI_pred_DP_AL|SpliceAI_pred_DP_DG|SpliceAI_pred_DP_DL|SpliceAI_pred_DS_AG|SpliceAI_pred_DS_AL|SpliceAI_pred_DS_DG|SpliceAI_pred_DS_DL|SpliceAI_pred_SYMBOL|CAPICE_CL|CAPICE_SC|HPO|IncompletePenetrance|InheritanceModesGene|VKGL_CL|ASV_ACMG_class|ASV_AnnotSV_ranking_criteria|ASV_AnnotSV_ranking_score|gnomAD|gnomAD_AF|gnomAD_HN|VIPC|VIPP|VIPL">
+##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakend">
+##INFO=<ID=MATE_BND_DEPTH,Number=1,Type=Integer,Description="Read depth at remote translocation mate breakend">
+##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
+##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
+##INFO=<ID=gnomAD,Number=.,Type=String,Description="/groups/solve-rd/tmp10/vip/resources/GRCh37/gnomad.total.r2.1.1.sites.stripped.vcf.gz (exact)">
+##INFO=<ID=gnomAD_AF,Number=.,Type=String,Description="AF field from /groups/solve-rd/tmp10/vip/resources/GRCh37/gnomad.total.r2.1.1.sites.stripped.vcf.gz">
+##INFO=<ID=gnomAD_HN,Number=.,Type=String,Description="HN field from /groups/solve-rd/tmp10/vip/resources/GRCh37/gnomad.total.r2.1.1.sites.stripped.vcf.gz">
+##IncompletePenetrance=Boolean indicating if the gene is known for incomplete penetrance.
+##InheritanceModesGene=List of inheritance modes for the gene
+##SpliceAI_pred_DP_AG=SpliceAI predicted effect on splicing. Delta position for acceptor gain
+##SpliceAI_pred_DP_AL=SpliceAI predicted effect on splicing. Delta position for acceptor loss
+##SpliceAI_pred_DP_DG=SpliceAI predicted effect on splicing. Delta position for donor gain
+##SpliceAI_pred_DP_DL=SpliceAI predicted effect on splicing. Delta position for donor loss
+##SpliceAI_pred_DS_AG=SpliceAI predicted effect on splicing. Delta score for acceptor gain
+##SpliceAI_pred_DS_AL=SpliceAI predicted effect on splicing. Delta score for acceptor loss
+##SpliceAI_pred_DS_DG=SpliceAI predicted effect on splicing. Delta score for donor gain
+##SpliceAI_pred_DS_DL=SpliceAI predicted effect on splicing. Delta score for donor loss
+##SpliceAI_pred_SYMBOL=SpliceAI gene symbol
+##VEP="v105" time="2022-03-25 13:12:21" cache="/groups/solve-rd/tmp10/vip/resources/vep/cache/homo_sapiens_refseq/105_GRCh37" ensembl-io=105.2a0a40c ensembl=105.525fbcb ensembl-variation=105.ac8178e ensembl-funcgen=105.660df8f 1000genomes="phase3" COSMIC="92" ClinVar="202012" HGMD-PUBLIC="20204" assembly="GRCh37.p13" dbSNP="154" gencode="GENCODE 19" genebuild="2011-04" gnomAD="r2.1" polyphen="2.2.2" refseq="2020-10-26 17:03:42 - GCF_000001405.25_GRCh37.p13_genomic.gff" regbuild="1.0" sift="sift5.2.2"
+##VIPC=VIP decision tree classification
+##VIPL=VIP decision tree labels (ampersand separated)
+##VIPP=VIP decision tree path (ampersand separated)
+##VIP_Command=nextflow run ./main.nf --input /groups/solve-rd/tmp10/testdata/testdata_b37_noSample.vcf --output /groups/solve-rd/tmp10/testdata_out/ --keep --phenotypes 'HP:0000951' --assembly GRCh37
+##VIP_Version=4.0.1
+##VIP_treeCommand=--input testdata_b37_noSample_chunk0_annotated.vcf.gz --config /groups/solve-rd/tmp10/vip/resources/decision_tree.json --labels 0 --path 0 --output testdata_b37_noSample_chunk0_classified.vcf.gz
+##VIP_treeVersion=2.2.0
+##VKGL_CL=VKGL consensus variant classification.
+##contig=<ID=1,length=249250621,assembly=b37>
+##contig=<ID=2,length=243199373,assembly=b37>
+##contig=<ID=3,length=198022430,assembly=b37>
+##contig=<ID=4,length=191154276,assembly=b37>
+##contig=<ID=5,length=180915260,assembly=b37>
+##contig=<ID=6,length=171115067,assembly=b37>
+##contig=<ID=7,length=159138663,assembly=b37>
+##contig=<ID=8,length=146364022,assembly=b37>
+##contig=<ID=9,length=141213431,assembly=b37>
+##contig=<ID=10,length=135534747,assembly=b37>
+##contig=<ID=11,length=135006516,assembly=b37>
+##contig=<ID=12,length=133851895,assembly=b37>
+##contig=<ID=13,length=115169878,assembly=b37>
+##contig=<ID=14,length=107349540,assembly=b37>
+##contig=<ID=15,length=102531392,assembly=b37>
+##contig=<ID=16,length=90354753,assembly=b37>
+##contig=<ID=17,length=81195210,assembly=b37>
+##contig=<ID=18,length=78077248,assembly=b37>
+##contig=<ID=19,length=59128983,assembly=b37>
+##contig=<ID=20,length=63025520,assembly=b37>
+##contig=<ID=21,length=48129895,assembly=b37>
+##contig=<ID=22,length=51304566,assembly=b37>
+##contig=<ID=X,length=155270560,assembly=b37>
+##contig=<ID=Y,length=59373566,assembly=b37>
+##contig=<ID=MT,length=16569,assembly=b37>
+##fileDate=20200320
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+1	10042538	.	C	T	.	PASS	CSQ=T|missense_variant|MODERATE|NMNAT1|64802|Transcript|NM_001297778.1|protein_coding|5/5||NM_001297778.1:c.619C>T|NP_001284707.1:p.Arg207Trp|778/3796|619/840|207/279|R/W|Cgg/Tgg|rs142968179&CM127756|1||1||1|EntrezGene|||||0.04|0.08||pathogenic||1&1|26103963&22842229&22842230|||||||0|-36|-16|17|0.00|0.00|0.00|0.00|NMNAT1|VUS|0.16572298|||AR|LP||||1:10042538-10042538|3.88948e-05|0|P|filter&vkgl&exit_p|,T|downstream_gene_variant|MODIFIER|NMNAT1|64802|Transcript|NM_001297779.2|protein_coding||||||||||rs142968179&CM127756|1|714|1|||EntrezGene||||||||pathogenic||1&1|26103963&22842229&22842230|||||||0|-36|-16|17|0.00|0.00|0.00|0.00|NMNAT1|VUS|0.033541594|||AR|LP||||1:10042538-10042538|3.88948e-05|0|P|filter&vkgl&exit_p|,T|missense_variant|MODERATE|NMNAT1|64802|Transcript|NM_022787.4|protein_coding|5/5||NM_022787.4:c.619C>T|NP_073624.2:p.Arg207Trp|716/3734|619/840|207/279|R/W|Cgg/Tgg|rs142968179&CM127756|1||1|||EntrezGene|||||0.04|0.08||pathogenic||1&1|26103963&22842229&22842230|||||||0|-36|-16|17|0.00|0.00|0.00|0.00|NMNAT1|VUS|0.14321531|||AR|LP||||1:10042538-10042538|3.88948e-05|0|P|filter&vkgl&exit_p|
+1	16376412	n_alt	G	N	.	PASS	CSQ=N|splice_donor_variant|HIGH|CLCNKB|1188|Transcript|NM_000085.5|protein_coding||10/19||||||||CS1211892&CS971662|1||1||1|EntrezGene||||||||||1&1|||||||||||||||||VUS|0.373989|HP:0000951||AR||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,N|splice_donor_variant|HIGH|CLCNKB|1188|Transcript|NM_001165945.2|protein_coding||3/12||||||||CS1211892&CS971662|1||1|||EntrezGene||||||||||1&1|||||||||||||||||VUS|0.373989|HP:0000951||AR||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|
+1	17349219	n_ref	N	A	.	PASS	CSQ=A|coding_sequence_variant|MODIFIER|SDHB|6390|Transcript|NM_003000.3|protein_coding|7/8||NM_003000.3:c.649C>T||662/1015|649/843|217/280||Ngc/Tgc|CM094752&CM1210440&COSV64965760|1||-1||1|EntrezGene|||||||||0&0&1|1&1&1|||||||||||||||||VUS|0.48189265|HP:0000951||AD&AR||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|
+1	17349219	g_ref	G	A	.	PASS	CSQ=A|missense_variant|MODERATE|SDHB|6390|Transcript|NM_003000.3|protein_coding|7/8||NM_003000.3:c.649C>T|NP_002991.2:p.Arg217Cys|662/1015|649/843|217/280|R/C|Cgc/Tgc|rs200245469&CM094752&CM1210440&COSV64965760|1||-1||1|EntrezGene|||||0|1||likely_pathogenic|0&0&0&1|1&1&1&1||||||||28|6|6|5|0.00|0.00|0.00|0.00|SDHB|VUS|0.89070946|HP:0000951||AD&AR|LP|||||||P|filter&vkgl&exit_p|
+1	152520788	symbolic1	A	<DEL>	.	PASS	CSQ=deletion|transcript_ablation|HIGH|LCE3D|84648|Transcript|NM_032563.2|protein_coding|||||||||||1||-1||1|EntrezGene|||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,deletion|upstream_gene_variant|MODIFIER|LCE3C|353144|Transcript|NM_178434.3|protein_coding|||||||||||1|2608|1|||EntrezGene|||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,deletion|transcript_ablation|HIGH|LCE3E|353145|Transcript|NM_178435.4|protein_coding|||||||||||1||-1|||EntrezGene|||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000946440||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001787329||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000013752||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000946442||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000946443||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001505919||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001787330||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001787331||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001787332||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00701519957||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00905971885||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00522719201||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|;SVLEN=-49314;SVTYPE=DEL
+2	47635667	symbolic2	G	<INS>	.	PASS	CSQ=insertion|splice_polypyrimidine_tract_variant&coding_sequence_variant&intron_variant&feature_elongation|LOW|MSH2|4436|Transcript|NM_000251.3|protein_coding|2-8/16|2-8/15|||376-?/3115|340-?/2805|114-?/934||||1||1||1|EntrezGene|||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|splice_polypyrimidine_tract_variant&coding_sequence_variant&intron_variant&feature_elongation|LOW|MSH2|4436|Transcript|NM_001258281.1|protein_coding|3-9/17|3-9/16|||281-?/3025|142-?/2607|48-?/868||||1||1|||EntrezGene|||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001919953||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001919954||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001919955||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001619621||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001919956||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001619622||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001919957||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00530589128||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00530502780||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00525298438||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00530512660||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00530431919||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00522077931||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00533275472||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00530460887||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00530563027||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00530550696||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00530602292||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00522015626||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00533060686||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00525131899||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00530576102||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00530666750||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00521962166||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00530450113||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00530544207||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00530711816||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00530598979||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00530595684||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00530473938||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00530525851||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00530621224||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00522057275||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00530464197||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00530443827||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00530506057||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00530582758||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00530663480||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00907424037||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00530647393||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00521890195||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00530480339||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00525492134||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00530592365||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00530618016||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00530477292||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00907390759||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00533222876||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00530556431||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00530547368||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00530457296||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00530627902||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00530559755||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00530566326||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00530529094||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00792006282||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00530691966||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00530435489||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00530427760||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00532972809||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00530519223||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00530579454||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00530695223||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00530467446||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00530572820||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00530585944||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00530605579||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00530453303||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00530655502||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00530446920||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00530492633||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00532804158||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00908072887||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00776750923||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00907553345||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00530470669||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00907757558||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00530509374||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00530515926||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00522584830||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00525790028||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|;SVLEN=-49314;SVTYPE=INS
+4	106320294	.	G	A	.	PASS	CSQ=A|missense_variant|MODERATE|PPA2|27068|Transcript|NM_006903.4|protein_coding|7/11||NM_006903.4:c.596C>T|NP_008834.3:p.Pro199Leu|616/1586|596/918|199/305|P/L|cCg/cTg|rs138215926&CM1610192&COSV58994362|1||-1|||EntrezGene|||||0|0.985||pathogenic|0&0&1|1&1&1|27523597|||||||-34|27|-2|-43|0.00|0.00|0.00|0.00|PPA2|VUS|0.8097311|||AR|LP||||4:106320294-106320294|0.000211803|0|P|filter&vkgl&exit_p|,A|missense_variant|MODERATE|PPA2|27068|Transcript|NM_176866.2|protein_coding|4/8||NM_176866.2:c.377C>T|NP_789842.2:p.Pro126Leu|397/1367|377/699|126/232|P/L|cCg/cTg|rs138215926&CM1610192&COSV58994362|1||-1|||EntrezGene|||||0|0.992||pathogenic|0&0&1|1&1&1|27523597|||||||-34|27|-2|-43|0.00|0.00|0.00|0.00|PPA2|VUS|0.7550335|||AR|LP||||4:106320294-106320294|0.000211803|0|P|filter&vkgl&exit_p|,A|missense_variant|MODERATE|PPA2|27068|Transcript|NM_176867.3|protein_coding|2/6||NM_176867.3:c.185C>T|NP_789843.2:p.Pro62Leu|205/1175|185/507|62/168|P/L|cCg/cTg|rs138215926&CM1610192&COSV58994362|1||-1|||EntrezGene|||||0|0.995||pathogenic|0&0&1|1&1&1|27523597|||||||-34|27|-2|-43|0.00|0.00|0.00|0.00|PPA2|VUS|0.8145551|||AR|LP||||4:106320294-106320294|0.000211803|0|P|filter&vkgl&exit_p|,A|missense_variant|MODERATE|PPA2|27068|Transcript|NM_176869.3|protein_coding|8/12||NM_176869.3:c.683C>T|NP_789845.1:p.Pro228Leu|695/1665|683/1005|228/334|P/L|cCg/cTg|rs138215926&CM1610192&COSV58994362|1||-1||1|EntrezGene|||||0|0.993||pathogenic|0&0&1|1&1&1|27523597|||||||-34|27|-2|-43|0.00|0.00|0.00|0.00|PPA2|VUS|0.76490384|||AR|LP||||4:106320294-106320294|0.000211803|0|P|filter&vkgl&exit_p|,A|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001994744|promoter_flanking_region||||||||||rs138215926&CM1610192&COSV58994362|1|||||||||||||pathogenic|0&0&1|1&1&1|27523597|||||||||||||||||||||||||4:106320294-106320294|0.000211803|0|P|filter&vkgl&clinVar&exit_p|
+7	42017311	single_breakend_nation	C	C.	.	PASS	CSQ=BND|coding_sequence_variant|MODIFIER|GLI3|2737|Transcript|NM_000168.6|protein_coding|12/15||||1938/8405|1657/4743|553/1580||||1||-1||1|EntrezGene|||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,BND|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001394462||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,BND|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000325885||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|;SVTYPE=BND
+7	42064957	.	GACTC	G	.	PASS	CSQ=-|frameshift_variant|HIGH|GLI3|2737|Transcript|NM_000168.6|protein_coding|9/15||NM_000168.6:c.1258_1261del|NP_000159.3:p.Glu420LeufsTer3|1539-1542/8405|1258-1261/4743|420-421/1580|ES/X|GAGTct/ct||1||-1||1|EntrezGene||||||||||||||||||18|21|-40|6|0.00|0.00|0.00|0.00|GLI3|VUS|0.9822135||1|AD|LP|||||||P|filter&vkgl&exit_p|
+8	61765143	breakend1	G	]11:134014225]G	.	PASS	BND_DEPTH=26;CSQ=BND|intron_variant|MODIFIER|CHD7|55636|Transcript|NM_001316690.1|protein_coding||2/4|||||||||1||1|||EntrezGene|||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,BND|coding_sequence_variant|MODIFIER|CHD7|55636|Transcript|NM_017780.4|protein_coding|30/38||||6499/11606|5982/8994|1994/2997||||1||1||1|EntrezGene|||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,BND|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000225105||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|;MATEID=breakend2;MATE_BND_DEPTH=39;SVTYPE=BND
+8	145140500	.	CAG	C	.	PASS	CSQ=-|frameshift_variant|HIGH|GPAA1|8733|Transcript|NM_003801.4|protein_coding|11/12||NM_003801.4:c.1477_1478del|NP_003792.1:p.Arg493GlyfsTer152|1574-1575/2054|1477-1478/1866|493/621|R/X|AGg/g|rs782339984|1||1||1|EntrezGene||||||||pathogenic||1||||||||-15|-8|12|-21|0.02|0.00|0.00|0.00|GPAA1|VUS|0.99260485|||AR|LP||||8:145140501-145140503|0.000142617|0|P|filter&vkgl&exit_p|,-|downstream_gene_variant|MODIFIER|EXOSC4|54512|Transcript|NM_019037.3|protein_coding||||||||||rs782339984|1|4950|1|||EntrezGene||||||||pathogenic||1||||||||-15|-8|12|-21|0.02|0.00|0.00|0.00|GPAA1|VUS|0.14952277||||||||8:145140501-145140503|0.000142617|0|P|filter&vkgl&clinVar&exit_p|
+9	107546633	.	AAAGAT	A	.	PASS	CSQ=-|frameshift_variant|HIGH|ABCA1|19|Transcript|NM_005502.4|protein_coding|50/50||NM_005502.4:c.6744_6748del|NP_005493.2:p.Phe2250ThrfsTer3|7057-7061/10408|6744-6748/6786|2248-2250/2261|TSF/TX|acATCTTtt/actt||1||-1||1|EntrezGene|||||||||||||||||||||||||||VUS|0.9823047|HP:0000951||AD&AR||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|
+10	126091499	.	G	C	.	PASS	CSQ=C|stop_gained|HIGH|OAT|4942|Transcript|NM_000274.4|protein_coding|7/10||NM_000274.4:c.897C>G|NP_000265.1:p.Tyr299Ter|977/2039|897/1320|299/439|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808|||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.979408|||AR|LP||||10:126091499-126091499|1.59133e-05|0|P|filter&vkgl&exit_p|,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001171814.2|protein_coding|6/9||NM_001171814.2:c.483C>G|NP_001165285.1:p.Tyr161Ter|749/1811|483/906|161/301|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808|||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.97846687|||AR|LP||||10:126091499-126091499|1.59133e-05|0|P|filter&vkgl&exit_p|,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322965.2|protein_coding|7/10||NM_001322965.2:c.897C>G|NP_001309894.1:p.Tyr299Ter|972/2034|897/1320|299/439|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808|||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.979408|||AR|LP||||10:126091499-126091499|1.59133e-05|0|P|filter&vkgl&exit_p|,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322966.2|protein_coding|8/11||NM_001322966.2:c.897C>G|NP_001309895.1:p.Tyr299Ter|1292/2354|897/1320|299/439|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1||1|EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808|||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.9796912|||AR|LP||||10:126091499-126091499|1.59133e-05|0|P|filter&vkgl&exit_p|,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322967.2|protein_coding|8/11||NM_001322967.2:c.897C>G|NP_001309896.1:p.Tyr299Ter|1097/2159|897/1320|299/439|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808|||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.9819772|||AR|LP||||10:126091499-126091499|1.59133e-05|0|P|filter&vkgl&exit_p|,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322968.2|protein_coding|9/12||NM_001322968.2:c.897C>G|NP_001309897.1:p.Tyr299Ter|1184/2246|897/1320|299/439|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808|||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.9819772|||AR|LP||||10:126091499-126091499|1.59133e-05|0|P|filter&vkgl&exit_p|,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322969.2|protein_coding|8/11||NM_001322969.2:c.897C>G|NP_001309898.1:p.Tyr299Ter|1064/2126|897/1320|299/439|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808|||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.9819772|||AR|LP||||10:126091499-126091499|1.59133e-05|0|P|filter&vkgl&exit_p|,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322970.2|protein_coding|9/12||NM_001322970.2:c.897C>G|NP_001309899.1:p.Tyr299Ter|1280/2342|897/1320|299/439|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808|||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.9796912|||AR|LP||||10:126091499-126091499|1.59133e-05|0|P|filter&vkgl&exit_p|,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322971.2|protein_coding|5/8||NM_001322971.2:c.576C>G|NP_001309900.1:p.Tyr192Ter|656/1718|576/999|192/332|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808|||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.9760591|||AR|LP||||10:126091499-126091499|1.59133e-05|0|P|filter&vkgl&exit_p|,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322974.2|protein_coding|7/10||NM_001322974.2:c.297C>G|NP_001309903.1:p.Tyr99Ter|863/1925|297/720|99/239|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808|||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.9775237|||AR|LP||||10:126091499-126091499|1.59133e-05|0|P|filter&vkgl&exit_p|
+11	134014225	breakend2	G	G[8:61765143[	.	PASS	BND_DEPTH=39;CSQ=BND|intron_variant|MODIFIER|JAM3|83700|Transcript|NM_001205329.2|protein_coding||3/7|||||||||1||1|||EntrezGene|||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,BND|coding_sequence_variant|MODIFIER|JAM3|83700|Transcript|NM_032801.5|protein_coding|4/9||||359/3765|347/933|116/310||||1||1||1|EntrezGene|||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|;MATEID=breakend1;MATE_BND_DEPTH=26;SVTYPE=BND
+13	77570128	.	G	A	.	PASS	CSQ=A|missense_variant|MODERATE|CLN5|1203|Transcript|NM_001366624.2|protein_coding|3/5||NM_001366624.2:c.431G>A|NP_001353553.1:p.Cys144Tyr|449/5286|431/594|144/197|C/Y|tGt/tAt|rs1566219136|1||1|||EntrezGene|||||0|0.995||pathogenic||1||||||||-27|-43|-27|-1|0.00|0.00|0.01|0.00|CLN5|VUS|0.79378206|||AR|LP|||||||P|filter&vkgl&exit_p|,A|missense_variant|MODERATE|CLN5|1203|Transcript|NM_006493.4|protein_coding|3/4||NM_006493.4:c.431G>A|NP_006484.2:p.Cys144Tyr|449/5243|431/1077|144/358|C/Y|tGt/tAt|rs1566219136|1||1||1|EntrezGene|||||0|0.999||pathogenic||1||||||||-27|-43|-27|-1|0.00|0.00|0.01|0.00|CLN5|VUS|0.862269|||AR|LP|||||||P|filter&vkgl&exit_p|
+14	89336407	.	TG	T	.	PASS	CSQ=-|frameshift_variant|HIGH|TTC8|123016|Transcript|NM_001288781.1|protein_coding|12/16||NM_001288781.1:c.963del|NP_001275710.1:p.Met321IlefsTer15|1159/2378|963/1596|321/531|M/X|atG/at|rs1431207606|1||1||1|EntrezGene||||||||||||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.9807489|HP:0000951||AR|LP||||14:89336408-89336409|1.19537e-05|0|P|filter&vkgl&exit_p|,-|frameshift_variant|HIGH|TTC8|123016|Transcript|NM_001288782.1|protein_coding|10/14||NM_001288782.1:c.321del|NP_001275711.1:p.Met107IlefsTer15|1079/2298|321/954|107/317|M/X|atG/at|rs1431207606|1||1|||EntrezGene||||||||||||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.9838007|HP:0000951||AR|LP||||14:89336408-89336409|1.19537e-05|0|P|filter&vkgl&exit_p|,-|frameshift_variant|HIGH|TTC8|123016|Transcript|NM_001288783.1|protein_coding|11/15||NM_001288783.1:c.198del|NP_001275712.1:p.Met66IlefsTer15|1051/2270|198/831|66/276|M/X|atG/at|rs1431207606|1||1|||EntrezGene||||||||||||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.98078203|HP:0000951||AR|LP||||14:89336408-89336409|1.19537e-05|0|P|filter&vkgl&exit_p|,-|frameshift_variant|HIGH|TTC8|123016|Transcript|NM_001366535.2|protein_coding|10/13||NM_001366535.2:c.885del|NP_001353464.1:p.Met295IlefsTer15|942/5160|885/1434|295/477|M/X|atG/at|rs1431207606|1||1|||EntrezGene||||||||||||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.9797095|HP:0000951||AR|LP||||14:89336408-89336409|1.19537e-05|0|P|filter&vkgl&exit_p|,-|frameshift_variant|HIGH|TTC8|123016|Transcript|NM_001366536.2|protein_coding|9/12||NM_001366536.2:c.795del|NP_001353465.1:p.Met265IlefsTer15|852/5070|795/1344|265/447|M/X|atG/at|rs1431207606|1||1|||EntrezGene||||||||||||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.9856574|HP:0000951||AR|LP||||14:89336408-89336409|1.19537e-05|0|P|filter&vkgl&exit_p|,-|frameshift_variant|HIGH|TTC8|123016|Transcript|NM_144596.4|protein_coding|11/15||NM_144596.4:c.915del|NP_653197.2:p.Met305IlefsTer15|972/2183|915/1548|305/515|M/X|atG/at|rs1431207606|1||1|||EntrezGene||||||||||||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.9619866|HP:0000951||AR|LP||||14:89336408-89336409|1.19537e-05|0|P|filter&vkgl&exit_p|,-|frameshift_variant|HIGH|TTC8|123016|Transcript|NM_198309.3|protein_coding|11/15||NM_198309.3:c.885del|NP_938051.1:p.Met295IlefsTer15|1081/2300|885/1518|295/505|M/X|atG/at|rs1431207606|1||1|||EntrezGene||||||||||||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.9801349|HP:0000951||AR|LP||||14:89336408-89336409|1.19537e-05|0|P|filter&vkgl&exit_p|,-|frameshift_variant|HIGH|TTC8|123016|Transcript|NM_198310.3|protein_coding|10/14||NM_198310.3:c.795del|NP_938052.1:p.Met265IlefsTer15|991/2210|795/1428|265/475|M/X|atG/at|rs1431207606|1||1|||EntrezGene||||||||||||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.9853147|HP:0000951||AR|LP||||14:89336408-89336409|1.19537e-05|0|P|filter&vkgl&exit_p|,-|non_coding_transcript_exon_variant|MODIFIER|TTC8|123016|Transcript|NR_159362.2|misc_RNA|11/15||NR_159362.2:n.1002del||1002/5304|||||rs1431207606|1||1|||EntrezGene||||||||||||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.10411882|HP:0000951||AR|LP||||14:89336408-89336409|1.19537e-05|0|P|filter&vkgl&exit_p|
+14	105167860	.	T	G	.	PASS	CSQ=G|missense_variant|MODERATE|INF2|64423|Transcript|NM_001031714.4|protein_coding|2/22||NM_001031714.4:c.158T>G|NP_001026884.3:p.Leu53Arg|289/7566|158/3723|53/1240|L/R|cTg/cGg||1||1|||EntrezGene|||||0|0.999||||||||||||-28|-2|37|-2|0.00|0.00|0.00|0.00|INF2|VUS|0.9012849|||AD|LP|||||||P|filter&vkgl&exit_p|,G|missense_variant|MODERATE|INF2|64423|Transcript|NM_022489.4|protein_coding|2/23||NM_022489.4:c.158T>G|NP_071934.3:p.Leu53Arg|289/7623|158/3750|53/1249|L/R|cTg/cGg||1||1||1|EntrezGene|||||0|0.999||||||||||||-28|-2|37|-2|0.00|0.00|0.00|0.00|INF2|VUS|0.9012849|||AD|LP|||||||P|filter&vkgl&exit_p|,G|missense_variant|MODERATE|INF2|64423|Transcript|NM_032714.3|protein_coding|2/5||NM_032714.3:c.158T>G|NP_116103.1:p.Leu53Arg|289/1692|158/705|53/234|L/R|cTg/cGg||1||1|||EntrezGene|||||0|0.999||||||||||||-28|-2|37|-2|0.00|0.00|0.00|0.00|INF2|VUS|0.9012849|||AD|LP|||||||P|filter&vkgl&exit_p|,G|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001573054|open_chromatin_region|||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|
+17	29556064	.	AC	A	.	PASS	CSQ=-|frameshift_variant|HIGH|NF1|4763|Transcript|NM_000267.3|protein_coding|21/57||NM_000267.3:c.2433del|NP_000258.1:p.Ile812LeufsTer9|2816/12362|2433/8457|811/2818|T/X|acC/ac||1||1|||EntrezGene|||||||1|||||||||||-22|-11|12|25|0.00|0.00|0.00|0.00|NF1|VUS|0.9913782|HP:0000951|1|AD|LP|||||||P|filter&vkgl&exit_p|,-|frameshift_variant|HIGH|NF1|4763|Transcript|NM_001042492.3|protein_coding|21/58||NM_001042492.3:c.2433del|NP_001035957.1:p.Ile812LeufsTer9|2766/12373|2433/8520|811/2839|T/X|acC/ac||1||1||1|EntrezGene|||||||1|||||||||||-22|-11|12|25|0.00|0.00|0.00|0.00|NF1|VUS|0.9913782|HP:0000951|1|AD|LP|||||||P|filter&vkgl&exit_p|
+17	29663879	.	T	G	.	PASS	CSQ=G|missense_variant|MODERATE|NF1|4763|Transcript|NM_000267.3|protein_coding|41/57||NM_000267.3:c.6311T>G|NP_000258.1:p.Leu2104Arg|6694/12362|6311/8457|2104/2818|L/R|cTg/cGg|CM141499&CM143458|1||1|||EntrezGene|||||0|0.994||||1&1||||||||-42|41|-34|8|0.00|0.00|0.00|0.00|NF1|VUS|0.8564539|HP:0000951|1|AD|LP|||||||P|filter&vkgl&exit_p|,G|missense_variant|MODERATE|NF1|4763|Transcript|NM_001042492.3|protein_coding|42/58||NM_001042492.3:c.6374T>G|NP_001035957.1:p.Leu2125Arg|6707/12373|6374/8520|2125/2839|L/R|cTg/cGg|CM141499&CM143458|1||1||1|EntrezGene|||||0|0.993||||1&1||||||||-42|41|-34|8|0.00|0.00|0.00|0.00|NF1|VUS|0.8564539|HP:0000951|1|AD|LP|||||||P|filter&vkgl&exit_p|
+19	11216146	.	C	G	.	PASS	CSQ=G|stop_gained|HIGH|LDLR|3949|Transcript|NM_000527.5|protein_coding|4/18||NM_000527.5:c.564C>G|NP_000518.1:p.Tyr188Ter|650/5173|564/2583|188/860|Y/*|taC/taG|rs121908034&CM920416&COSV99370340|1||1||1|EntrezGene||||||||pathogenic/likely_pathogenic&pathogenic|0&0&1|1&1&1|25741868&27765764&17142622&8882879&1734722&10422803|||||||1|11|0|-14|0.00|0.00|0.00|0.00|LDLR|VUS|0.97590667|HP:0000951||AD&AR|LP|||||||P|filter&vkgl&exit_p|,G|stop_gained|HIGH|LDLR|3949|Transcript|NM_001195798.2|protein_coding|4/18||NM_001195798.2:c.564C>G|NP_001182727.1:p.Tyr188Ter|650/5167|564/2577|188/858|Y/*|taC/taG|rs121908034&CM920416&COSV99370340|1||1|||EntrezGene||||||||pathogenic/likely_pathogenic&pathogenic|0&0&1|1&1&1|25741868&27765764&17142622&8882879&1734722&10422803|||||||1|11|0|-14|0.00|0.00|0.00|0.00|LDLR|VUS|0.97590667|HP:0000951||AD&AR|LP|||||||P|filter&vkgl&exit_p|,G|stop_gained|HIGH|LDLR|3949|Transcript|NM_001195799.2|protein_coding|3/17||NM_001195799.2:c.441C>G|NP_001182728.1:p.Tyr147Ter|527/5050|441/2460|147/819|Y/*|taC/taG|rs121908034&CM920416&COSV99370340|1||1|||EntrezGene||||||||pathogenic/likely_pathogenic&pathogenic|0&0&1|1&1&1|25741868&27765764&17142622&8882879&1734722&10422803|||||||1|11|0|-14|0.00|0.00|0.00|0.00|LDLR|VUS|0.9765647|HP:0000951||AD&AR|LP|||||||P|filter&vkgl&exit_p|,G|intron_variant|MODIFIER|LDLR|3949|Transcript|NM_001195800.2|protein_coding||3/15|NM_001195800.2:c.314-1922C>G|||||||rs121908034&CM920416&COSV99370340|1||1|||EntrezGene||||||||pathogenic/likely_pathogenic&pathogenic|0&0&1|1&1&1|25741868&27765764&17142622&8882879&1734722&10422803|||||||1|11|0|-14|0.00|0.00|0.00|0.00|LDLR|VUS|0.0055715204|HP:0000951||AD&AR|LP|||||||P|filter&vkgl&exit_p|,G|intron_variant|MODIFIER|LDLR|3949|Transcript|NM_001195803.2|protein_coding||3/15|NM_001195803.2:c.314-1095C>G|||||||rs121908034&CM920416&COSV99370340|1||1|||EntrezGene||||||||pathogenic/likely_pathogenic&pathogenic|0&0&1|1&1&1|25741868&27765764&17142622&8882879&1734722&10422803|||||||1|11|0|-14|0.00|0.00|0.00|0.00|LDLR|VUS|0.0055715204|HP:0000951||AD&AR|LP|||||||P|filter&vkgl&exit_p|
+19	17451997	.	GA	G	.	PASS	CSQ=-|frameshift_variant|HIGH|GTPBP3|84705|Transcript|NM_001128855.3|protein_coding|8/9||NM_001128855.3:c.1058del|NP_001122327.1:p.Asn353ThrfsTer26|1117/2503|1058/1416|353/471|N/X|aAc/ac||1||1|||EntrezGene|||||||1|||||||||||34|33|-7|33|0.01|0.00|0.00|0.00|GTPBP3|VUS|0.9804278|HP:0000951||AR|LP|||||||P|filter&vkgl&exit_p|,-|frameshift_variant|HIGH|GTPBP3|84705|Transcript|NM_001195422.1|protein_coding|8/9||NM_001195422.1:c.1187del|NP_001182351.1:p.Asn396ThrfsTer26|1209/2595|1187/1545|396/514|N/X|aAc/ac||1||1|||EntrezGene|||||||1|||||||||||34|33|-7|33|0.01|0.00|0.00|0.00|GTPBP3|VUS|0.98119754|HP:0000951||AR|LP|||||||P|filter&vkgl&exit_p|,-|frameshift_variant|HIGH|GTPBP3|84705|Transcript|NM_032620.4|protein_coding|8/9||NM_032620.4:c.1121del|NP_116009.2:p.Asn374ThrfsTer26|1180/2566|1121/1479|374/492|N/X|aAc/ac||1||1|||EntrezGene|||||||1|||||||||||34|33|-7|33|0.01|0.00|0.00|0.00|GTPBP3|VUS|0.98185974|HP:0000951||AR|LP|||||||P|filter&vkgl&exit_p|,-|frameshift_variant|HIGH|GTPBP3|84705|Transcript|NM_133644.4|protein_coding|7/8||NM_133644.4:c.1217del|NP_598399.2:p.Asn406ThrfsTer26|1276/2662|1217/1575|406/524|N/X|aAc/ac||1||1||1|EntrezGene|||||||1|||||||||||34|33|-7|33|0.01|0.00|0.00|0.00|GTPBP3|VUS|0.97986597|HP:0000951||AR|LP|||||||P|filter&vkgl&exit_p|,-|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001610216|CTCF_binding_site|||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,-|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001909308|promoter|||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,-|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00523665928||||||||||||1||1||||||||||||||||ENSPFM0305|8|N||HOXB2::ELF1||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|
+20	62326992	.	C	T	.	PASS	CSQ=T|downstream_gene_variant|MODIFIER|ARFRP1|10139|Transcript|NM_001134758.4|protein_coding||||||||||rs993254667|1|3008|-1|||EntrezGene|||||||||||||||||||||||||||VUS|0.030849965||||||||20:62326992-62326992|1.62113e-05|0|P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,T|downstream_gene_variant|MODIFIER|ARFRP1|10139|Transcript|NM_001267544.3|protein_coding||||||||||rs993254667|1|3008|-1|||EntrezGene|||||||||||||||||||||||||||VUS|0.030849965||||||||20:62326992-62326992|1.62113e-05|0|P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,T|downstream_gene_variant|MODIFIER|ARFRP1|10139|Transcript|NM_001267545.3|protein_coding||||||||||rs993254667|1|3008|-1|||EntrezGene|||||||||||||||||||||||||||VUS|0.030849965||||||||20:62326992-62326992|1.62113e-05|0|P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,T|downstream_gene_variant|MODIFIER|ARFRP1|10139|Transcript|NM_001267546.3|protein_coding||||||||||rs993254667|1|3008|-1|||EntrezGene|||||||||||||||||||||||||||VUS|0.030849965||||||||20:62326992-62326992|1.62113e-05|0|P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,T|downstream_gene_variant|MODIFIER|ARFRP1|10139|Transcript|NM_001267547.3|protein_coding||||||||||rs993254667|1|3008|-1|||EntrezGene|||||||||||||||||||||||||||VUS|0.030849965||||||||20:62326992-62326992|1.62113e-05|0|P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,T|downstream_gene_variant|MODIFIER|ARFRP1|10139|Transcript|NM_001267548.3|protein_coding||||||||||rs993254667|1|3008|-1|||EntrezGene|||||||||||||||||||||||||||VUS|0.030849965||||||||20:62326992-62326992|1.62113e-05|0|P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,T|downstream_gene_variant|MODIFIER|ARFRP1|10139|Transcript|NM_001267549.3|protein_coding||||||||||rs993254667|1|3008|-1|||EntrezGene|||||||||||||||||||||||||||VUS|0.030849965||||||||20:62326992-62326992|1.62113e-05|0|P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,T|missense_variant|MODERATE|RTEL1|51750|Transcript|NM_001283009.2|protein_coding|34/35||NM_001283009.2:c.3811C>T|NP_001269938.1:p.Arg1271Trp|4136/4615|3811/3903|1271/1300|R/W|Cgg/Tgg|rs993254667|1||1||1|EntrezGene|||||0.16|0.003||||||||||||12|-21|44|11|0.00|0.00|0.00|0.09|RTEL1|VUS|0.010304764|HP:0000951||AD&AR|||||20:62326992-62326992|1.62113e-05|0|P|filter&vkgl&clinVar&gnomad&effect&sift&polyphen&exit_p|,T|intron_variant|MODIFIER|RTEL1|51750|Transcript|NM_001283010.1|protein_coding||33/33|NM_001283010.1:c.2984-139C>T|||||||rs993254667|1||1|||EntrezGene||||||||||||||||||12|-21|44|11|0.00|0.00|0.00|0.09|RTEL1|VUS|0.0033220313|HP:0000951||AD&AR|||||20:62326992-62326992|1.62113e-05|0|P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,T|downstream_gene_variant|MODIFIER|ARFRP1|10139|Transcript|NM_003224.6|protein_coding||||||||||rs993254667|1|3008|-1|||EntrezGene|||||||||||||||||||||||||||VUS|0.030849965||||||||20:62326992-62326992|1.62113e-05|0|P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,T|upstream_gene_variant|MODIFIER|TNFRSF6B|8771|Transcript|NM_003823.4|protein_coding||||||||||rs993254667|1|1013|1|||EntrezGene|||||||||||||||||||||||||||VUS|0.010661138||||||||20:62326992-62326992|1.62113e-05|0|P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,T|intron_variant|MODIFIER|RTEL1|51750|Transcript|NM_016434.4|protein_coding||34/34|NM_016434.4:c.3653-139C>T|||||||rs993254667|1||1|||EntrezGene||||||||||||||||||12|-21|44|11|0.00|0.00|0.00|0.09|RTEL1|VUS|0.0033220313|HP:0000951||AD&AR|||||20:62326992-62326992|1.62113e-05|0|P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,T|intron_variant|MODIFIER|RTEL1|51750|Transcript|NM_032957.5|protein_coding||34/34|NM_032957.5:c.3725-139C>T|||||||rs993254667|1||1|||EntrezGene||||||||||||||||||12|-21|44|11|0.00|0.00|0.00|0.09|RTEL1|VUS|0.0033220313|HP:0000951||AD&AR|||||20:62326992-62326992|1.62113e-05|0|P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,T|non_coding_transcript_exon_variant|MODIFIER|RTEL1-TNFRSF6B|100533107|Transcript|NR_037882.1|lncRNA|34/38||NR_037882.1:n.4638C>T||4638/5772|||||rs993254667|1||1|||EntrezGene||||||||||||||||||12|-21|44|11|0.00|0.00|0.00|0.09|RTEL1-TNFRSF6B|VUS|0.06427667||||||||20:62326992-62326992|1.62113e-05|0|P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,T|downstream_gene_variant|MODIFIER|ARFRP1|10139|Transcript|NR_051954.3|misc_RNA||||||||||rs993254667|1|3008|-1|||EntrezGene|||||||||||||||||||||||||||VUS|0.030849965||||||||20:62326992-62326992|1.62113e-05|0|P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,T|downstream_gene_variant|MODIFIER|ARFRP1|10139|Transcript|NR_051955.3|misc_RNA||||||||||rs993254667|1|3008|-1|||EntrezGene|||||||||||||||||||||||||||VUS|0.030849965||||||||20:62326992-62326992|1.62113e-05|0|P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,T|downstream_gene_variant|MODIFIER|ARFRP1|10139|Transcript|NR_051956.3|misc_RNA||||||||||rs993254667|1|3008|-1|||EntrezGene|||||||||||||||||||||||||||VUS|0.030849965||||||||20:62326992-62326992|1.62113e-05|0|P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,T|downstream_gene_variant|MODIFIER|ARFRP1|10139|Transcript|NR_051957.3|misc_RNA||||||||||rs993254667|1|3008|-1|||EntrezGene|||||||||||||||||||||||||||VUS|0.030849965||||||||20:62326992-62326992|1.62113e-05|0|P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,T|downstream_gene_variant|MODIFIER|ARFRP1|10139|Transcript|NR_051958.3|misc_RNA||||||||||rs993254667|1|3008|-1|||EntrezGene|||||||||||||||||||||||||||VUS|0.030849965||||||||20:62326992-62326992|1.62113e-05|0|P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|
+22	50627593	.	C	CTG	.	.	CSQ=TG|intron_variant|MODIFIER|TRABD|80305|Transcript|NM_001320484.2|protein_coding||1/9|NM_001320484.2:c.-35+3188_-35+3189insTG||||||||1||1||1|EntrezGene|||||||||||||||||||||||||||VUS|0.008963062|||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,TG|intron_variant|MODIFIER|TRABD|80305|Transcript|NM_001320485.2|protein_coding||1/9|NM_001320485.2:c.-35+3188_-35+3189insTG||||||||1||1|||EntrezGene|||||||||||||||||||||||||||VUS|0.008963062|||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,TG|upstream_gene_variant|MODIFIER|TRABD|80305|Transcript|NM_001320487.2|protein_coding|||||||||||1|1422|1|||EntrezGene|||||||||||||||||||||||||||VUS|0.2446478|||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,TG|upstream_gene_variant|MODIFIER|TRABD|80305|Transcript|NM_001320488.2|protein_coding|||||||||||1|1422|1|||EntrezGene|||||||||||||||||||||||||||VUS|0.2446478|||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,TG|intron_variant|MODIFIER|TRABD|80305|Transcript|NM_001378762.1|protein_coding||1/9|NM_001378762.1:c.-35+3119_-35+3120insTG||||||||1||1|||EntrezGene|||||||||||||||||||||||||||VUS|0.008963062|||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,TG|intron_variant|MODIFIER|TRABD|80305|Transcript|NM_001378765.1|protein_coding||1/10|NM_001378765.1:c.-35+3159_-35+3160insTG||||||||1||1|||EntrezGene|||||||||||||||||||||||||||VUS|0.008963062|||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,TG|intron_variant|MODIFIER|TRABD|80305|Transcript|NM_025204.4|protein_coding||1/9|NM_025204.4:c.-35+3163_-35+3164insTG||||||||1||1|||EntrezGene|||||||||||||||||||||||||||VUS|0.008963062|||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,TG|intron_variant&non_coding_transcript_variant|MODIFIER|TRABD|80305|Transcript|NR_135275.2|misc_RNA||1/9|NR_135275.2:n.64+3188_64+3189insTG||||||||1||1|||EntrezGene|||||||||||||||||||||||||||VUS|0.03393742|||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,TG|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000147691|promoter|||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|
+22	50721546	.	C	T	.	PASS	CSQ=T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376864.1|protein_coding|17/37||NM_001376864.1:c.2749G>A|NP_001363793.1:p.Gly917Ser|2881/6611|2749/5754|917/1917|G/S|Ggc/Agc|rs1377653283|1||-1||1|EntrezGene||||||||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.14842245||||||||22:50721546-50721546|4.49665e-06|0|P|filter&vkgl&clinVar&gnomad&effect&sift&polyphen&impact&exit_p|,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376865.1|protein_coding|18/38||NM_001376865.1:c.2818G>A|NP_001363794.1:p.Gly940Ser|2898/6391|2818/5586|940/1861|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene||||||||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.14842245||||||||22:50721546-50721546|4.49665e-06|0|P|filter&vkgl&clinVar&gnomad&effect&sift&polyphen&impact&exit_p|,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376866.1|protein_coding|17/37||NM_001376866.1:c.2749G>A|NP_001363795.1:p.Gly917Ser|2909/6402|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.92206705||||||||22:50721546-50721546|4.49665e-06|0|LP|filter&vkgl&clinVar&gnomad&effect&sift&exit_lp|,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376867.1|protein_coding|18/38||NM_001376867.1:c.2749G>A|NP_001363796.1:p.Gly917Ser|2969/6462|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.92206705||||||||22:50721546-50721546|4.49665e-06|0|LP|filter&vkgl&clinVar&gnomad&effect&sift&exit_lp|,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376868.1|protein_coding|18/38||NM_001376868.1:c.2749G>A|NP_001363797.1:p.Gly917Ser|2962/6455|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.92206705||||||||22:50721546-50721546|4.49665e-06|0|LP|filter&vkgl&clinVar&gnomad&effect&sift&exit_lp|,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376869.1|protein_coding|16/36||NM_001376869.1:c.2749G>A|NP_001363798.1:p.Gly917Ser|2856/6349|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.92206705||||||||22:50721546-50721546|4.49665e-06|0|LP|filter&vkgl&clinVar&gnomad&effect&sift&exit_lp|,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376870.1|protein_coding|17/37||NM_001376870.1:c.2749G>A|NP_001363799.1:p.Gly917Ser|2881/6374|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.92206705||||||||22:50721546-50721546|4.49665e-06|0|LP|filter&vkgl&clinVar&gnomad&effect&sift&exit_lp|,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376871.1|protein_coding|17/37||NM_001376871.1:c.2749G>A|NP_001363800.1:p.Gly917Ser|2874/6367|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.92206705||||||||22:50721546-50721546|4.49665e-06|0|LP|filter&vkgl&clinVar&gnomad&effect&sift&exit_lp|,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376872.1|protein_coding|19/39||NM_001376872.1:c.2749G>A|NP_001363801.1:p.Gly917Ser|3066/6559|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.92206705||||||||22:50721546-50721546|4.49665e-06|0|LP|filter&vkgl&clinVar&gnomad&effect&sift&exit_lp|,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376873.1|protein_coding|18/38||NM_001376873.1:c.2749G>A|NP_001363802.1:p.Gly917Ser|3218/6711|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.92206705||||||||22:50721546-50721546|4.49665e-06|0|LP|filter&vkgl&clinVar&gnomad&effect&sift&exit_lp|,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376874.1|protein_coding|18/38||NM_001376874.1:c.2749G>A|NP_001363803.1:p.Gly917Ser|2934/6427|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.92206705||||||||22:50721546-50721546|4.49665e-06|0|LP|filter&vkgl&clinVar&gnomad&effect&sift&exit_lp|,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376875.1|protein_coding|16/36||NM_001376875.1:c.2749G>A|NP_001363804.1:p.Gly917Ser|2933/6426|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.92206705||||||||22:50721546-50721546|4.49665e-06|0|LP|filter&vkgl&clinVar&gnomad&effect&sift&exit_lp|,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376876.1|protein_coding|18/38||NM_001376876.1:c.2749G>A|NP_001363805.1:p.Gly917Ser|2927/6420|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.92206705||||||||22:50721546-50721546|4.49665e-06|0|LP|filter&vkgl&clinVar&gnomad&effect&sift&exit_lp|,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376877.1|protein_coding|18/38||NM_001376877.1:c.2749G>A|NP_001363806.1:p.Gly917Ser|3198/6691|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.92206705||||||||22:50721546-50721546|4.49665e-06|0|LP|filter&vkgl&clinVar&gnomad&effect&sift&exit_lp|,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376878.1|protein_coding|16/36||NM_001376878.1:c.2749G>A|NP_001363807.1:p.Gly917Ser|2821/6314|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.92206705||||||||22:50721546-50721546|4.49665e-06|0|LP|filter&vkgl&clinVar&gnomad&effect&sift&exit_lp|,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376879.1|protein_coding|19/39||NM_001376879.1:c.2749G>A|NP_001363808.1:p.Gly917Ser|3101/6594|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.92206705||||||||22:50721546-50721546|4.49665e-06|0|LP|filter&vkgl&clinVar&gnomad&effect&sift&exit_lp|,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376880.1|protein_coding|17/37||NM_001376880.1:c.2749G>A|NP_001363809.1:p.Gly917Ser|2991/6484|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.92206705||||||||22:50721546-50721546|4.49665e-06|0|LP|filter&vkgl&clinVar&gnomad&effect&sift&exit_lp|,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376881.1|protein_coding|18/38||NM_001376881.1:c.2749G>A|NP_001363810.1:p.Gly917Ser|3046/6539|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.92206705||||||||22:50721546-50721546|4.49665e-06|0|LP|filter&vkgl&clinVar&gnomad&effect&sift&exit_lp|,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376882.1|protein_coding|17/37||NM_001376882.1:c.2749G>A|NP_001363811.1:p.Gly917Ser|3165/6658|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.92206705||||||||22:50721546-50721546|4.49665e-06|0|LP|filter&vkgl&clinVar&gnomad&effect&sift&exit_lp|,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376883.1|protein_coding|17/37||NM_001376883.1:c.2749G>A|NP_001363812.1:p.Gly917Ser|2881/6350|2749/5493|917/1830|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene||||||||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.14842245||||||||22:50721546-50721546|4.49665e-06|0|P|filter&vkgl&clinVar&gnomad&effect&sift&polyphen&impact&exit_p|,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376884.1|protein_coding|16/36||NM_001376884.1:c.2749G>A|NP_001363813.1:p.Gly917Ser|2821/6236|2749/5439|917/1812|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene||||||||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.14842245||||||||22:50721546-50721546|4.49665e-06|0|P|filter&vkgl&clinVar&gnomad&effect&sift&polyphen&impact&exit_p|,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376885.1|protein_coding|17/37||NM_001376885.1:c.2749G>A|NP_001363814.1:p.Gly917Ser|2909/6324|2749/5439|917/1812|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene||||||||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.14842245||||||||22:50721546-50721546|4.49665e-06|0|P|filter&vkgl&clinVar&gnomad&effect&sift&polyphen&impact&exit_p|,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376886.1|protein_coding|17/37||NM_001376886.1:c.2656G>A|NP_001363815.1:p.Gly886Ser|2876/6369|2656/5424|886/1807|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene||||||||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.14842245||||||||22:50721546-50721546|4.49665e-06|0|P|filter&vkgl&clinVar&gnomad&effect&sift&polyphen&impact&exit_p|,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_012401.4|protein_coding|17/37||NM_012401.4:c.2749G>A|NP_036533.2:p.Gly917Ser|2916/6409|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.92206705||||||||22:50721546-50721546|4.49665e-06|0|LP|filter&vkgl&clinVar&gnomad&effect&sift&exit_lp|,T|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001960812|promoter||||||||||rs1377653283|1|||||||||||||||||||||||||||||||||||||||||22:50721546-50721546|4.49665e-06|0|P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|
+X	48933021	x_chrom	A	T	.	PASS	CSQ=T|splice_donor_variant|HIGH|WDR45|11152|Transcript|NM_001029896.2|protein_coding||9/10|NM_001029896.2:c.827+2T>A|||||||CS135341|1||-1|||EntrezGene||||||||||1||||||||27|28|-2|2|0.02|0.00|0.01|0.99|WDR45|VUS|0.9700852|HP:0000951||XL|LP|||||||P|filter&vkgl&exit_p|,T|splice_donor_variant|HIGH|WDR45|11152|Transcript|NM_007075.4|protein_coding||10/11|NM_007075.4:c.830+2T>A|||||||CS135341|1||-1||1|EntrezGene||||||||||1||||||||27|28|-2|2|0.02|0.00|0.01|0.99|WDR45|VUS|0.9700852|HP:0000951||XL|LP|||||||P|filter&vkgl&exit_p|,T|upstream_gene_variant|MODIFIER|PRAF2|11230|Transcript|NM_007213.3|protein_coding||||||||||CS135341|1|1360|-1|||EntrezGene||||||||||1||||||||27|28|-2|2|0.02|0.00|0.01|0.99|WDR45|VUS|0.0149048455|||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&exit_p|,T|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001477865|CTCF_binding_site||||||||||CS135341|1|||||||||||||||1|||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,T|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001765299|promoter_flanking_region||||||||||CS135341|1|||||||||||||||1|||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|
+Y	2655641	y_chrom	G	A	.	PASS	CSQ=A|stop_gained|HIGH|SRY|6736|Transcript|NM_003140.3|protein_coding|1/1||NM_003140.3:c.4C>T|NP_003131.1:p.Gln2Ter|83/828|4/615|2/204|Q/*|Caa/Taa|rs104894977&CM981858|1||-1||1|EntrezGene||||||||pathogenic||1&1|2401216&9443877|||||||-26|-50|2|-4|0.01|0.00|0.00|0.00|SRY|VUS|0.8890525|||||||||||P|filter&vkgl&clinVar&exit_p|
+MT	15326	mt_chrom	A	G	.	PASS	CSQ=G|intergenic_variant|MODIFIER|||||||||||||||rs2853508|1||||1|||||||||benign&likely_pathogenic||1|31267007||||||||||||||||||||||||||||P|filter&vkgl&clinVar&exit_p|