@molgenis/vip-report-template 5.5.5 → 5.6.0

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 (8) hide show
  1. package/.travis.yml +1 -1
  2. package/package.json +3 -3
  3. package/src/App.tsx +7 -0
  4. package/src/components/record/RecordDownload.tsx +21 -2
  5. package/src/components/record/info/InheritanceModes.tsx +2 -2
  6. package/src/mocks/GRCh37/vcf/family.vcf.blob +2 -2
  7. package/src/utils/ApiUtils.ts +6 -1
  8. package/src/views/Help.tsx +13 -0
package/.travis.yml CHANGED
@@ -2,7 +2,7 @@ os: linux
2
2
  dist: focal
3
3
  language: node_js
4
4
  node_js:
5
- - lts/*
5
+ - 18
6
6
  branches:
7
7
  only:
8
8
  - main
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@molgenis/vip-report-template",
3
- "version": "5.5.5",
3
+ "version": "5.6.0",
4
4
  "description": "Report Template for Variant Call Format (VCF) Report Generator",
5
5
  "scripts": {
6
6
  "build": "vite build",
@@ -36,8 +36,8 @@
36
36
  "dependencies": {
37
37
  "@fortawesome/fontawesome-svg-core": "^6.4.2",
38
38
  "@fortawesome/free-solid-svg-icons": "^6.4.2",
39
- "@molgenis/vip-report-api": "^4.4.4",
40
- "@molgenis/vip-report-vcf": "^1.4.4",
39
+ "@molgenis/vip-report-api": "^4.5.0",
40
+ "@molgenis/vip-report-vcf": "^1.5.0",
41
41
  "@solidjs/router": "^0.8.3",
42
42
  "base64-js": "^1.5.1",
43
43
  "igv": "^2.15.10",
package/src/App.tsx CHANGED
@@ -17,6 +17,7 @@ import api from "./Api";
17
17
  import { DatasetDropdown } from "./components/DatasetDropdown";
18
18
  import SampleVariantConsequenceData from "./views/data/SampleVariantConsequenceData";
19
19
  import VariantConsequenceData from "./views/data/VariantConsequenceData";
20
+ import { Help } from "./views/Help";
20
21
 
21
22
  const App: Component = () => {
22
23
  const navigate = useNavigate();
@@ -57,6 +58,11 @@ const App: Component = () => {
57
58
  </Link>
58
59
  {api.isDatasetSupport() && <DatasetDropdown />}
59
60
  </div>
61
+ <div class="navbar-end">
62
+ <Link class="navbar-item" href="/help">
63
+ Help
64
+ </Link>
65
+ </div>
60
66
  </div>
61
67
  </nav>
62
68
  <div class="container is-fluid">
@@ -91,6 +97,7 @@ const App: Component = () => {
91
97
  </Route>
92
98
  </Route>
93
99
  </Route>
100
+ <Route path="/help" element={<Help />} />
94
101
  </Routes>
95
102
  </ErrorBoundary>
96
103
  </div>
package/src/components/record/RecordDownload.tsx CHANGED
@@ -4,7 +4,6 @@ import { Metadata } from "@molgenis/vip-report-vcf/src/Vcf";
4
4
  import api from "../../Api";
5
5
  import { Filter, writeVcf } from "@molgenis/vip-report-vcf/src/VcfWriter";
6
6
 
7
- const DOWNLOAD_POSTFIX = "_report.vcf";
8
7
  export const RecordDownload: Component<{ recordsMetadata: Metadata; query?: Query; samples?: Sample[] }> = (props) => {
9
8
  const filter = (): Filter | undefined =>
10
9
  props.samples ? { samples: props.samples.map((sample) => sample.person.individualId) } : undefined;
@@ -13,6 +12,26 @@ export const RecordDownload: Component<{ recordsMetadata: Metadata; query?: Quer
13
12
  return htsFile.uri.split("\\").pop()?.split("/").pop()?.split(".").shift();
14
13
  }
15
14
 
15
+ // derived from https://stackoverflow.com/a/19176102
16
+ function getDateTimeString() {
17
+ const now = new Date();
18
+
19
+ const year = now.getFullYear().toString();
20
+ let month = (now.getMonth() + 1).toString();
21
+ let day = now.getDate().toString();
22
+ let hour = now.getHours().toString();
23
+ let minute = now.getMinutes().toString();
24
+ let second = now.getSeconds().toString();
25
+
26
+ if (month.length == 1) month = "0" + month;
27
+ if (day.length == 1) day = "0" + day;
28
+ if (hour.length == 1) hour = "0" + hour;
29
+ if (minute.length == 1) minute = "0" + minute;
30
+ if (second.length == 1) second = "0" + second;
31
+
32
+ return year + month + day + "_" + hour + minute + second;
33
+ }
34
+
16
35
  function onClick() {
17
36
  const handler = async () => {
18
37
  const records = await api.getRecords({ query: props.query, size: Number.MAX_SAFE_INTEGER });
@@ -23,7 +42,7 @@ export const RecordDownload: Component<{ recordsMetadata: Metadata; query?: Quer
23
42
  link.href = url;
24
43
  const htsFile = await api.getHtsFileMetadata();
25
44
  const filename = parseFilename(htsFile) as string;
26
- link.setAttribute("download", filename + DOWNLOAD_POSTFIX);
45
+ link.setAttribute("download", filename + "_report_" + getDateTimeString() + ".vcf");
27
46
  document.body.appendChild(link);
28
47
  link.click();
29
48
  document.body.removeChild(link);
package/src/components/record/info/InheritanceModes.tsx CHANGED
@@ -4,9 +4,9 @@ import { FieldProps } from "../field/Field";
4
4
  import { FieldMultipleValue } from "../field/FieldMultipleValue";
5
5
 
6
6
  export const InheritanceModes: Component<FieldProps> = (props) => {
7
- const inheritanceModesGene: string | null = props.info.value as ValueString;
7
+ const inheritanceModesGene: ValueString[] = props.info.value as ValueString[];
8
8
  let isArInheritance = false;
9
- if (inheritanceModesGene === null || inheritanceModesGene.includes("AR")) {
9
+ if (inheritanceModesGene.includes("AR") || inheritanceModesGene.length === 0) {
10
10
  isArInheritance = props.context.isPossibleCompound !== undefined && props.context.isPossibleCompound;
11
11
  }
12
12
  return (
package/src/mocks/GRCh37/vcf/family.vcf.blob CHANGED
@@ -102,7 +102,7 @@
102
102
  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|0.9882061||||||HP:0000951||1.439||AR||LP||||4.909000|1:16376412-16376412|6.38086e-05|0|1285112|Pathogenic/Likely_pathogenic||no_assertion_criteria_provided|LP|chrom&gene&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|0.9882061||||||HP:0000951||1.439||AR||LP||||4.909000|1:16376412-16376412|6.38086e-05|0|1285112|Pathogenic/Likely_pathogenic||no_assertion_criteria_provided|LP|chrom&gene&filter&vkgl&exit_lp;VIPC_S=OK GT:AD:DP:GQ:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S:VIS 0|1:50:50:50:AR:1_16375583_GA_G,1_16376412_G_N:0:1188:1:OK,OK:HR&GQ&DP&VIM&exit_ok,HR&GQ&DP&VIM&exit_ok:AR_C 0|0:50,0:50:50:.:.:.:.:.:.:.:. 1|0:25,25:50:50:.:.:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.:.:.
103
103
  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||||||||180|28|6|6|5|0.00|0.00|0.00|0.00|SDHB|VUS|0.9769107||||||HP:0000951||2.452||AD&AR||LP||||9.093000||||183735|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|chrom&gene&filter&vkgl&exit_lp;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIG:VIM:VIPC_S:VIPP_S 1|1:0,50:50:50:AR:1:6390:1:OK:HR&GQ&DP&VIM&exit_ok 1|0:45,5:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 1|0:25,25:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.
104
104
  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|0.991252||||||HP:0000951||2.452||AD&AR||LP||||7.131000|1:17355094-17355094|1.19344e-05|0|29896|Pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|chrom&gene&filter&vkgl&exit_lp;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIG:VIM:VIPC_S:VIPP_S 1|0:5,45:50:50:AD:1:6390:1:OK:HR&GQ&DP&VIM&exit_ok 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.
105
- 1 152520788 symbolic1 A <DEL> . PASS CSQ=deletion|transcript_ablation|HIGH|LCE3D|84648|Transcript|NM_032563.2|protein_coding|||||||||||1||-1||1|EntrezGene|||||||||||||||||||||||||||||||||||||||||||||||||||||VUS|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&annotSV&spliceAI&utr5&capice&exit_vus,deletion|upstream_gene_variant|MODIFIER|LCE3C|353144|Transcript|NM_178434.3|protein_coding|||||||||||1|2608|1|||EntrezGene|||||||||||||||||||||||||||||||||||||||||||||||||||||VUS|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&annotSV&spliceAI&utr5&capice&exit_vus,deletion|transcript_ablation|HIGH|LCE3E|353145|Transcript|NM_178435.4|protein_coding|||||||||||1||-1|||EntrezGene|||||||||||||||||||||||||||||||||||||||||||||||||||||VUS|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&annotSV&spliceAI&utr5&capice&exit_vus,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000946440||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001787329||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000013752||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000946442||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000946443||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001505919||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001787330||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001787331||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001787332||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00701519957||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00905971885||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00522719201||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm;SVLEN=-49314;SVTYPE=DEL;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIM:VIPC_S:VIPP_S 1|1:0,50:50:50:AR:1:0:OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK:HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok 0|0:50,0:50:50:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:. 1|0:25,25:50:50:.:.:.:.:.
105
+ 1 152520788 symbolic1 A <DEL> . PASS CSQ=deletion|transcript_ablation|HIGH|LCE3D|84648|Transcript|NM_032563.2|protein_coding|||||||||||1||-1||1|EntrezGene|||||||||||||||||||||||||||||||||||||||||||||||||||||VUS|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&annotSV&spliceAI&utr5&capice&exit_vus,deletion|upstream_gene_variant|MODIFIER|LCE3C|353144|Transcript|NM_178434.3|protein_coding|||||||||||1|2608|1|||EntrezGene|||||||||||||||||||||||||||||||||||||||||||||||||||||VUS|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&annotSV&spliceAI&utr5&capice&exit_vus,deletion|transcript_ablation|HIGH|LCE3E|353145|Transcript|NM_178435.4|protein_coding|||||||||||1||-1|||EntrezGene|||||||||||||||||||||||||||||||||||||||||||||||||||||VUS|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&annotSV&spliceAI&utr5&capice&exit_vus,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000946440||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001787329||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000013752||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000946442||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000946443||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001505919||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001787330||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001787331||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001787332||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00701519957||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00905971885||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00522719201||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm;SVLEN=-49314;SVTYPE=DEL;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIM:VIPC_S:VIPP_S:VIC 1|1:0,50:50:50:AR:1:0:OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK:HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok:123456_A_C 0|0:50,0:50:50:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:. 1|0:25,25:50:50:.:.:.:.:.
106
106
  2 321682 . T <DEL> . PASS CSQ=deletion|non_coding_transcript_exon_variant&intron_variant&feature_truncation|MODIFIER|LINC01865|105373350|Transcript|NR_146953.1|lncRNA|3/4|3/3|||685-?/2100||||||1||1||1|EntrezGene||||||||||||||||||||||||||||||||||||||||||3|1A_(cf_Gene_count%2C_RE_gene%2C_+0.00)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(1_gene%2C_+0.00)%3B5F_(+0.00)|0.0|||||||||VUS|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&annotSV&exit_vus;END=321887;SVLEN=-205;SVTYPE=DEL;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIG:VIM:VIPC_S:VIPP_S 1|1:0,50:50:50:AR:0:64802:.:OK:HR&GQ&DP&VIM&VID&exit_ok 1|0:50,0:50:50:.:.:.:.:.:. 1|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.
107
107
  2 6693415 . T <DEL> . PASS CSQ=deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001914803||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524064657||||||||||||1||||1|||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524052275||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524121752||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524688093||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00525576244||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524108762||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524259723||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524175972||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524198224||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524134566||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00769910345||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524344258||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524278495||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524312437||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524083163||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524770333||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00829572188||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524396085||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00909212078||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524214908||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524150456||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524239498||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524095954||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00530094654||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|intergenic_variant|MODIFIER||||||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm;END=6707844;SVLEN=-14429;SVTYPE=DEL;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIG:VIM:VIPC_S:VIPP_S 1|1:0,50:50:50:AR:1:64802:0:OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK:HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.
108
108
  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|||||||98|-34|27|-2|-43|0.00|0.00|0.00|0.00|PPA2|VUS|0.7474259||||||||-1.922||AR||LP||||9.359000|4:106320294-106320294|0.000211803|0|372226|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|chrom&gene&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|||||||98|-34|27|-2|-43|0.00|0.00|0.00|0.00|PPA2|VUS|0.75460654||||||||-1.922||AR||LP||||9.359000|4:106320294-106320294|0.000211803|0|372226|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|chrom&gene&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|||||||98|-34|27|-2|-43|0.00|0.00|0.00|0.00|PPA2|VUS|0.89774835||||||||-1.922||AR||LP||||9.359000|4:106320294-106320294|0.000211803|0|372226|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|chrom&gene&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|||||||98|-34|27|-2|-43|0.00|0.00|0.00|0.00|PPA2|VUS|0.77676606||||||||-1.922||AR||LP||||9.359000|4:106320294-106320294|0.000211803|0|372226|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|chrom&gene&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||||||||||||||||||||||||||||||||||9.359000|4:106320294-106320294|0.000211803|0|372226|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LQ|chrom&gene&exit_rm;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIG:VIM:VIPC_S:VIPP_S 1|0:0,50:50:50:AD:1:27068:0:.:HR&GQ&DP&VIM&exit_ok,HR&GQ&DP&VIM&exit_ok,HR&GQ&DP&VIM&exit_ok,HR&GQ&DP&VIM&exit_ok,HR&GQ&DP&VIM&exit_ok 0|0:25,25:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 1|1:0,50:50:50:.:.:.:.:.:.
@@ -119,7 +119,7 @@
119
119
  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||||||||125|-48|2|28|-27|0.00|0.00|0.01|0.00|NF1|VUS|0.9277154||||||HP:0000951||0.583|1|AD||LP||||4.149000||||457686|Pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|chrom&gene&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||||||||125|-48|2|28|-27|0.00|0.00|0.01|0.00|NF1|VUS|0.97049046||||||HP:0000951||0.583|1|AD||LP||||4.149000||||457686|Pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|chrom&gene&filter&vkgl&exit_lp;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIM:VIPC_S:VIPP_S 1|1:0,50:50:.:AR:1:0:OK,OK:HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok 0|1:.:10:50:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.
120
120
  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||||||||102|-42|41|-34|8|0.00|0.00|0.00|0.00|NF1|VUS|0.99390525||||||HP:0000951||0.583|1|AD||LP||||7.536000||||996527|Likely_pathogenic||criteria_provided&_single_submitter|LP|chrom&gene&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||||||||102|-42|41|-34|8|0.00|0.00|0.00|0.00|NF1|VUS|0.9962404||||||HP:0000951||0.583|1|AD||LP||||7.536000||||996527|Likely_pathogenic||criteria_provided&_single_submitter|LP|chrom&gene&filter&vkgl&exit_lp;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIG:VIM:VIPC_S:VIPP_S:VIS 1|0:25,25:50:50:AD:0:4763:1:OK,OK:HR&GQ&DP&VIM&exit_ok,HR&GQ&DP&VIM&exit_ok:AD_IP 0|0:50,0:50:50:.:.:.:.:.:.:. 1|0:25,25:50:50:.:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.:.
121
121
  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|0.9976593||||||HP:0000951||0.583|1|AD||LP||||6.871000||||||||LP|chrom&gene&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|0.9986885||||||HP:0000951||0.583|1|AD||LP||||6.871000||||||||LP|chrom&gene&filter&vkgl&exit_lp;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIG:VIM:VIPC_S:VIPP_S:VIS .|.:25,25:50:50:AR,AD:0:4763:1:OK,OK:HR&GQ&DP&VIM&exit_ok,HR&GQ&DP&VIM&exit_ok:AR_C 0|0:50,0:50:50:.:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.:.
122
- 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.Val436_Ala437insGlyGlyArgSerGlyHisGly|1395-1396/5173|1309-1310/2583|437/860|A/VALDTEVA|gcc/gTCGCTCTGGACACGGAGGTGGcc||1||1||1|EntrezGene|||||||25|||||||||||||||||||||VUS|0.8812568|||||||HC|5.497||AD&AR||LP||||||||||||LP|chrom&gene&filter&vkgl&exit_lp;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIG:VIM:VIPC_S:VIPP_S 1|1:.:10:50:AR:0:3949:1:OK:HR&GQ&DP&VIM&exit_ok 0|1:.:10:50:.:.:.:.:.:. 1|0:25,25:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.
122
+ 19 11224051 . C CGTGGTCGCTCTGGACACGGAGCGTGGTCGCTCTGGACACGGAGCGTGGTCGCTCTGGACACGGAGCGTGGTCGCTCTGGACACGGAGCGTGGTCGCTCTGGACACGGAGCGTGGTCGCTCTGGACACGGAGCGTGGTCGCTCTGGACACGGAGCGTGGTCGCTCTGGACACGGAGCGTGGTCGCTCTGGACACGGAGCGTGGTCGCTCTGGACACGGAGCGTGGTCGCTCTGGACACGGAGCGTGGTCGCTCTGGACACGGAGCGTGGTCGCTCTGGACACGGAGCGTGGTCGCTCTGGACACGGAGCGTGGTCGCTCTGGACACGGAGCGTGGTCGCTCTGGACACGGAG . 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.Val436_Ala437insGlyGlyArgSerGlyHisGly|1395-1396/5173|1309-1310/2583|437/860|A/VALDTEVA|gcc/gTCGCTCTGGACACGGAGGTGGcc||1||1||1|EntrezGene|||||||25|||||||||||||||||||||VUS|0.8812568|||||||HC|5.497||AD&AR||LP||||||||||||LP|chrom&gene&filter&vkgl&exit_lp;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIG:VIM:VIPC_S:VIPP_S 1|1:.:10:50:AR:0:3949:1:OK:HR&GQ&DP&VIM&exit_ok 0|1:.:10:50:.:.:.:.:.:. 1|0:25,25:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.
123
123
  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||||||||64|-39|-47|-19|31|0.01|0.00|0.00|0.00|GTPBP3|VUS|0.92324424||||||HP:0000951||-1.926||AR||LP||||7.188000|19:17449399-17449399|7.96883e-06|0|488525|Conflicting_interpretations_of_pathogenicity||criteria_provided&_conflicting_interpretations|LP|chrom&gene&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||||||||64|-39|-47|-19|31|0.01|0.00|0.00|0.00|GTPBP3|VUS|0.65621275||||||HP:0000951||-1.926||AR||LP||||7.188000|19:17449399-17449399|7.96883e-06|0|488525|Conflicting_interpretations_of_pathogenicity||criteria_provided&_conflicting_interpretations|LP|chrom&gene&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|0.71450377||||||||-1.785||||||||7.188000|19:17449399-17449399|7.96883e-06|0|488525|Conflicting_interpretations_of_pathogenicity||criteria_provided&_conflicting_interpretations|LP|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&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||||||||64|-39|-47|-19|31|0.01|0.00|0.00|0.00|GTPBP3|VUS|0.84315056||||||HP:0000951||-1.926||AR||LP||||7.188000|19:17449399-17449399|7.96883e-06|0|488525|Conflicting_interpretations_of_pathogenicity||criteria_provided&_conflicting_interpretations|LP|chrom&gene&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||||||||64|-39|-47|-19|31|0.01|0.00|0.00|0.00|GTPBP3|VUS|0.8864299||||||HP:0000951||-1.926||AR||LP||||7.188000|19:17449399-17449399|7.96883e-06|0|488525|Conflicting_interpretations_of_pathogenicity||criteria_provided&_conflicting_interpretations|LP|chrom&gene&filter&vkgl&exit_lp,T|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000107883|promoter||||||||||rs774708853&COSV50176281|1|||||||||||||likely_pathogenic|0&1|1&1|||||||||||||||||||||||||||||||||||7.188000|19:17449399-17449399|7.96883e-06|0|488525|Conflicting_interpretations_of_pathogenicity||criteria_provided&_conflicting_interpretations|LQ|chrom&gene&exit_rm;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIM:VIPC_S:VIPP_S 1|0:25,25:50:50:AD:1:0:OK,OK,OK,OK,OK,OK:HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok 0|0:50,0:50:50:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.
124
124
  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|0.99768054||||||HP:0000951||-1.926||AR||LP||||5.586000||||||||LP|chrom&gene&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|0.99091107||||||HP:0000951||-1.926||AR||LP||||5.586000||||||||LP|chrom&gene&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|0.99607384||||||HP:0000951||-1.926||AR||LP||||5.586000||||||||LP|chrom&gene&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|0.9972447||||||HP:0000951||-1.926||AR||LP||||5.586000||||||||LP|chrom&gene&filter&vkgl&exit_lp,-|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001610216|CTCF_binding_site|||||||||||1||||||||||||||||||||||||||||||||||||||||||||||||||5.586000||||||||LQ|chrom&gene&exit_rm,-|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001909308|promoter|||||||||||1||||||||||||||||||||||||||||||||||||||||||||||||||5.586000||||||||LQ|chrom&gene&exit_rm,-|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00523665928||||||||||||1||1||||||||||||||||ENSPFM0305|8|N||HOXB2::ELF1||||||||||||||||||||||||||||5.586000||||||||LQ|chrom&gene&exit_rm;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIG:VIM:VIPC_S:VIPP_S 1|1:0,50:50:50:AR:1:84705:1:OK,OK,OK,OK,OK,OK,OK:HR&GQ&DP&VIM&exit_ok,HR&GQ&DP&VIM&exit_ok,HR&GQ&DP&VIM&exit_ok,HR&GQ&DP&VIM&exit_ok,HR&GQ&DP&VIM&exit_ok,HR&GQ&DP&VIM&exit_ok,HR&GQ&DP&VIM&exit_ok 0|0:10,0:10:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 1|0:25,25:50:50:.:.:.:.:.:. 1|1:0,50:50:50:.:.:.:.:.:. 1|1:0,50:50:50:.:.:.:.:.:.
125
125
  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||||||||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.14641568||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LB|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lb,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||||||||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.10027899||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LB|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lb,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||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.71265084||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&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||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.7664242||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&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||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.7664242||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&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||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.66974294||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&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||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.6837599||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&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||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.6837599||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&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||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.7025085||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&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||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.7267535||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&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||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.7664242||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&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||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.7664242||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&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||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.7664242||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&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||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.70509267||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&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||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.66974294||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&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||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.69429386||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&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||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.7664242||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&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||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.8251113||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&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||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.70509267||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&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||||||||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.10285367||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LB|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lb,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||||||||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.119815774||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LB|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lb,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||||||||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.114952855||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LB|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lb,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||||||||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.12163515||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LB|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lb,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||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.75893486||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp,T|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001960812|promoter||||||||||rs1377653283|1||||||||||||||||||||||||||||||||||||||||||||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LQ|chrom&gene&exit_rm;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIM:VIPC_S:VIPP_S 1|1:0,50:50:50:AR:1:0:OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK:HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok 0|0:10,0:10:50:.:.:.:.:. 1|0:25,25:50:50:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:. 1|0:25,25:50:50:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.
package/src/utils/ApiUtils.ts CHANGED
@@ -229,7 +229,12 @@ export async function fetchPhenotypicFeatures(sample: Item<Sample>): Promise<Phe
229
229
 
230
230
  export function getRecordLabel(item: Item<Record>) {
231
231
  const record = item.data;
232
- return `${record.c}:${record.p} ${record.a.map((a) => `${record.r}>${a !== null ? a : "."}`).join(" / ")}`;
232
+ return `${record.c}:${record.p} ${record.a
233
+ .map(
234
+ (a) =>
235
+ `${record.r}>${a !== null ? (a.length > 4 ? a.substring(0, 2) + "\u2026" + a.charAt(a.length - 1) : a) : "."}`,
236
+ )
237
+ .join(" / ")}`;
233
238
  }
234
239
 
235
240
  export const EMPTY_RECORD_ITEM: Item<Record> = {
package/src/views/Help.tsx ADDED
@@ -0,0 +1,13 @@
1
+ import { Component } from "solid-js";
2
+ import { Anchor } from "../components/Anchor";
3
+ export const Help: Component = () => {
4
+ return (
5
+ <>
6
+ <span>The documentation for the Variant Interpretation Pipeline is located </span>
7
+ <Anchor href={`https://molgenis.github.io/vip/`}>
8
+ <span>here</span>
9
+ </Anchor>
10
+ <span>.</span>
11
+ </>
12
+ );
13
+ };