@molgenis/vip-report-template 3.1.3 → 3.1.4

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 (4) hide show
  1. package/package.json +1 -1
  2. package/src/components/SampleTable.tsx +1 -1
  3. package/src/components/Sort.tsx +1 -1
  4. package/src/mocks/GRCh37/vcf/family.vcf.blob +6 -0
package/package.json CHANGED
@@ -1,6 +1,6 @@
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  {
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  "name": "@molgenis/vip-report-template",
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- "version": "3.1.3",
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+ "version": "3.1.4",
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  "description": "Report Template for Variant Call Format (VCF) Report Generator",
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  "scripts": {
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  "build": "vite build",
package/src/components/SampleTable.tsx CHANGED
@@ -76,7 +76,7 @@ export const SampleTable: Component<{
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  <For each={props.samples}>
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  {(sample) => (
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  <tr>
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- <td>{sample.id}</td>
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+ <td>{sample.data.person.familyId}</td>
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  <td>
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  <Link href={`/samples/${sample.id}`}>{sample.data.person.individualId}</Link>
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  </td>
package/src/components/Sort.tsx CHANGED
@@ -40,7 +40,7 @@ export const Sort: Component<{
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  <div class="field">
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  <div class="select">
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  <select onChange={onSortChange}>
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- <option value="-1" />
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+ <option value="-1">Position</option>
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  <For each={sortableOptions()}>
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  {(option, i) => (
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  <option value={i()} selected={option.selected === true}>
package/src/mocks/GRCh37/vcf/family.vcf.blob CHANGED
@@ -29,6 +29,9 @@
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  ##INFO=<ID=gnomAD,Number=.,Type=String,Description="/groups/solve-rd/tmp10/projects/vip/git/vip/resources/GRCh37/gnomad.total.r2.1.1.sites.stripped.vcf.gz (exact)">
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  ##INFO=<ID=gnomAD_AF,Number=.,Type=String,Description="AF field from /groups/solve-rd/tmp10/projects/vip/git/vip/resources/GRCh37/gnomad.total.r2.1.1.sites.stripped.vcf.gz">
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  ##INFO=<ID=gnomAD_HN,Number=.,Type=String,Description="HN field from /groups/solve-rd/tmp10/projects/vip/git/vip/resources/GRCh37/gnomad.total.r2.1.1.sites.stripped.vcf.gz">
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+ ##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
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+ ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
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+ ##INFO=<ID=VIPC_S,Number=.,Type=String,Description="VIP decision tree classification (samples).">
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  ##IncompletePenetrance=Boolean indicating if the gene is known for incomplete penetrance.
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  ##InheritanceModesGene=List of inheritance modes for the gene
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  ##SpliceAI_pred_DP_AG=SpliceAI predicted effect on splicing. Delta position for acceptor gain
@@ -76,6 +79,7 @@
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  ##contig=<ID=MT,length=16569,assembly=b37>
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  ##fileDate=20200320
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  #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Patient Father Mother Sister Nephew Unrelated
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+ 1 1701 . T C . PASS CSQ=C|intergenic_variant|MODIFIER||||||||||||||||1||||1||||||||||||||||||||||||||||||||||||||||||||P|exip_p;DP=131 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:.:.:.:.:.
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  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>Tblablablablablabla|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|37133|Pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|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|37133|Pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|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|37133|Pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|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:.:.:.:.:.
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  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|638508|Conflicting_interpretations_of_pathogenicity||criteria_provided&_conflicting_interpretations|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|638508|Conflicting_interpretations_of_pathogenicity||criteria_provided&_conflicting_interpretations|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:.:.:.:.:.:.
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  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:.:.:.:.:.:.
@@ -83,6 +87,8 @@
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  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&HP:0003124||AD&AR|LP|||||||183735|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|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:.:.:.:.:.
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  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:0003124||AD&AR|LP||||1:17355094-17355094|1.19344e-05|0|29896|Pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|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:.:.:.:.:.
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  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:.:.:.:.
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+ 2 321682 . T <DEL> . PASS CSQ=deletion|non_coding_transcript_exon_variant&intron_variant&feature_truncation|MODIFIER|LINC01865|105373350|Transcript|NR_146953.1|lncRNA|4/3|3/3|||685-?/2100||||||1||1||1|EntrezGene|||||||||||||||||||||||||||||||||3|1A_(+0.00)%3B3A_(1_gene%2C_+0.00)%3B5F_(+0.00)|0||||||||P|exip_p;END=321887;SVLEN=-205;SVTYPE=DEL 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:.:.:.:.:.
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+ 2 6693415 . T <DEL> . PASS CSQ=deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001914803||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524064657||||||||||||1||||1||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524052275||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524121752||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524688093||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00525576244||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524108762||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524259723||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524175972||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524198224||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524134566||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00769910345||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524344258||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524278495||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524312437||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524083163||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524770333||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00829572188||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524396085||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00909212078||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524214908||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524150456||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524239498||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524095954||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00530094654||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|intergenic_variant|MODIFIER||||||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p|;END=6707844;SVLEN=-14429;SVTYPE=DEL 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:.:.:.:.:.
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  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|372226|Likely_pathogenic||criteria_provided&_single_submitter|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|372226|Likely_pathogenic||criteria_provided&_single_submitter|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|372226|Likely_pathogenic||criteria_provided&_single_submitter|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|372226|Likely_pathogenic||criteria_provided&_single_submitter|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|372226|Likely_pathogenic||criteria_provided&_single_submitter|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:.:.:.:.:.
87
93
  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:.:.:.:.:.
88
94
  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:.:.:.:.:.