@molgenis/vip-report-template 5.1.1 → 5.1.3

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Files changed (11) hide show
  1. package/package.json +1 -1
  2. package/src/components/InfoCollapsablePane.tsx +17 -2
  3. package/src/components/VariantsSampleTable.tsx +14 -1
  4. package/src/components/filter/FilterAllelicBalance.tsx +2 -2
  5. package/src/components/filter/FilterIntegerVim.tsx +18 -4
  6. package/src/components/record/Info.tsx +4 -0
  7. package/src/components/record/field/Field.tsx +1 -0
  8. package/src/components/record/format/GenotypeField.tsx +1 -1
  9. package/src/components/record/info/InheritanceModes.tsx +22 -0
  10. package/src/mocks/GRCh37/vcf/family.vcf.blob +1 -1
  11. package/src/views/SampleVariants.tsx +13 -3
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
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  {
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  "name": "@molgenis/vip-report-template",
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- "version": "5.1.1",
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+ "version": "5.1.3",
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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/InfoCollapsablePane.tsx CHANGED
@@ -12,6 +12,7 @@ export const InfoCollapsablePane: Component<{
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  fields: FieldMetadata[];
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  record: Item<Record>;
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  htsFileMeta: HtsFileMetadata;
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+ isPossibleCompound?: boolean;
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  }> = (props) => {
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  const [collapsed, setCollapsed]: Signal<boolean> = createSignal(false);
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@@ -59,10 +60,24 @@ export const InfoCollapsablePane: Component<{
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  {(j() == 0 || collapsed()) &&
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  (isCsqInfo(field, "Consequence") ? (
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  <Link href={`${useLocation().pathname}/${props.record.id}/consequences/${j()}`}>
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- <Info info={value} infoMeta={field} context={props.htsFileMeta} />
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+ <Info
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+ info={value}
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+ infoMeta={field}
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+ context={{
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+ genomeAssembly: props.htsFileMeta.genomeAssembly,
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+ isPossibleCompound: props.isPossibleCompound,
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+ }}
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+ />
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  </Link>
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  ) : (
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- <Info info={value} infoMeta={field} context={props.htsFileMeta} />
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+ <Info
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+ info={value}
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+ infoMeta={field}
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+ context={{
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+ genomeAssembly: props.htsFileMeta.genomeAssembly,
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+ isPossibleCompound: props.isPossibleCompound,
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+ }}
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+ />
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  ))}
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  </>
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  )}
package/src/components/VariantsSampleTable.tsx CHANGED
@@ -11,6 +11,7 @@ import { FieldMetadata } from "@molgenis/vip-report-vcf/src/MetadataParser";
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  import { FieldHeader } from "./FieldHeader";
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  import { Abbr } from "./Abbr";
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  import { abbreviateHeader } from "../utils/field";
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+ import { ValueString } from "@molgenis/vip-report-vcf/src/ValueParser";
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  export const VariantsSampleTable: Component<{
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  item: Item<Sample>;
@@ -182,7 +183,19 @@ export const VariantsSampleTable: Component<{
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  </>
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  )}
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  </For>
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- <InfoCollapsablePane fields={props.nestedFields} record={record} htsFileMeta={props.htsFileMeta} />
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+ <Show when={proband()} keyed>
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+ {(proband) => (
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+ <InfoCollapsablePane
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+ fields={props.nestedFields}
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+ record={record}
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+ htsFileMeta={props.htsFileMeta}
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+ isPossibleCompound={
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+ record.data.s[proband.index]["VIC"] !== null &&
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+ record.data.s[proband.index]["VIC"] !== undefined
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+ }
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+ />
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+ )}
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+ </Show>
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  </tr>
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  )}
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  </For>
package/src/components/filter/FilterAllelicBalance.tsx CHANGED
@@ -13,8 +13,8 @@ export function getAllelicBalanceQuery(sampleIndex: number): ComposedQuery {
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  {
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  operator: "and",
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  args: [
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- { selector: ["s", sampleIndex, "VIAB"], operator: ">", args: 0.2 },
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- { selector: ["s", sampleIndex, "VIAB"], operator: "<", args: 0.8 },
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+ { selector: ["s", sampleIndex, "VIAB"], operator: ">=", args: 0.2 },
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+ { selector: ["s", sampleIndex, "VIAB"], operator: "<=", args: 0.8 },
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  ],
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  },
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  ],
package/src/components/filter/FilterIntegerVim.tsx CHANGED
@@ -11,9 +11,19 @@ export const FilterIntegerVim: Component<FilterProps> = (props) => {
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  props.onChange({
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  key: selectorKey(fieldSelector),
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  query: {
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- selector: fieldSelector,
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- operator: "==",
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- args: 1,
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+ operator: "or",
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+ args: [
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+ {
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+ selector: fieldSelector,
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+ operator: "==",
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+ args: 1,
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+ },
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+ {
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+ selector: fieldSelector,
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+ operator: "==",
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+ args: null,
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+ },
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+ ],
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  },
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  });
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  else props.onClear({ key: selectorKey(fieldSelector) });
@@ -21,7 +31,11 @@ export const FilterIntegerVim: Component<FilterProps> = (props) => {
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  return (
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  <div class="control">
24
- <Checkbox label="Inheritance: match" checked={props.query && props.query.args === 1} onChange={onFilterChange} />
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+ <Checkbox
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+ label="Inheritance: match"
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+ checked={props.query && props.query.args !== undefined}
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+ onChange={onFilterChange}
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+ />
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  </div>
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  );
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  };
package/src/components/record/Info.tsx CHANGED
@@ -9,6 +9,7 @@ import { ClinVar } from "./info/ClinVar";
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  import { GnomAD } from "./info/GnomAD";
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  import { isAnyCsqInfo, isCsqInfo } from "../../utils/csqUtils";
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  import { Vkgl } from "./info/Vkgl";
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+ import { InheritanceModes } from "./info/InheritanceModes";
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  export const Info: Component<{
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  info: FieldValue;
@@ -26,6 +27,9 @@ export const Info: Component<{
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  <Match when={isCsqInfo(props.infoMeta, "SYMBOL")}>
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  <Gene {...props} />
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  </Match>
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+ <Match when={isCsqInfo(props.infoMeta, "InheritanceModesGene")}>
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+ <InheritanceModes {...props} />
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+ </Match>
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  <Match when={isCsqInfo(props.infoMeta, "gnomAD_AF")}>
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  <GnomAD {...props} />
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  </Match>
package/src/components/record/field/Field.tsx CHANGED
@@ -20,6 +20,7 @@ export type FieldValue = {
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  export type FieldContext = {
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  genomeAssembly?: string;
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+ isPossibleCompound?: boolean;
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  };
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  export const Field: Component<FieldProps> = (props) => {
package/src/components/record/format/GenotypeField.tsx CHANGED
@@ -55,7 +55,7 @@ export const GenotypeField: Component<{
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  )}
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  </For>
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  <Show when={lowReadDepth || allelicImbalance}>
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- <abbr title={getTitle(lowReadDepth, allelicImbalance)} class="ml-1">
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+ <abbr title={getTitle(lowReadDepth, allelicImbalance)} class="ml-1 is-clickable">
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  <i class="fas fa-circle-exclamation has-text-danger" />
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  </abbr>
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  </Show>
package/src/components/record/info/InheritanceModes.tsx ADDED
@@ -0,0 +1,22 @@
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+ import { Component, Show } from "solid-js";
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+ import { Value, ValueString } from "@molgenis/vip-report-vcf/src/ValueParser";
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+ import { FieldProps } from "../field/Field";
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+ import { FieldMultipleValue } from "../field/FieldMultipleValue";
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+
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+ export const InheritanceModes: Component<FieldProps> = (props) => {
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+ const inheritanceModesGene: string | null = props.info.value as ValueString;
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+ let isArInheritance = false;
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+ if (inheritanceModesGene === null || inheritanceModesGene.includes("AR")) {
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+ isArInheritance = props.context.isPossibleCompound !== undefined && props.context.isPossibleCompound;
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+ }
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+ return (
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+ <>
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+ <FieldMultipleValue info={props.info.value as Value[]} infoMetadata={props.infoMeta} />
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+ <Show when={isArInheritance} keyed>
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+ <abbr title="Variant is possibly part of a compound." class="ml-1 is-clickable">
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+ <i class="fas fa-circle-exclamation has-text-info" />
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+ </abbr>
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+ </Show>
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+ </>
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+ );
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+ };
package/src/mocks/GRCh37/vcf/family.vcf.blob CHANGED
@@ -97,7 +97,7 @@
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  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|||||||623394|Pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|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|||||||623394|Pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp| GT:AD:DP:VIC:VID:VIM:GQ 1|1:0,50:50:.:1:0:50 1|1:0,50:50:.:.:.: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
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  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|997900|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|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|997900|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|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|997900|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|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|997900|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|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|997900|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|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|997900|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|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|997900|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|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|997900|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|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|997900|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp| GT:AD:DP:VI:VIC:VID:VIM:GQ 1|0:25,25:50:AD:.:1:0:50 0|0:50,0:50:.:.:.:.:50 0|0:50,0:50:.:.:.:.:50 0|0:50,0:50:.:.:.:.:50 0|0:50,0:50:.:.:.:.:50 0|0:50,0:50:.:.:.:.:50
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  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|||||||2531|Pathogenic||no_assertion_criteria_provided|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|||||||2531|Pathogenic||no_assertion_criteria_provided|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|||||||2531|Pathogenic||no_assertion_criteria_provided|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|||||||2531|Pathogenic||no_assertion_criteria_provided|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|||||||2531|Pathogenic||no_assertion_criteria_provided|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|||||||2531|Pathogenic||no_assertion_criteria_provided|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|||||||2531|Pathogenic||no_assertion_criteria_provided|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|||||||2531|Pathogenic||no_assertion_criteria_provided|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|||||||2531|Pathogenic||no_assertion_criteria_provided|LP|filter&vkgl&exit_lp| GT:AD:DP:VI:VIC:VID:VIG:VIM:GQ 1|1:0,9:9:AR:.:0:123016:1:50 0|1:.:10:.:.:.:.:.:50 0|1:50:50:.:.:.:.:.:50 0|0:50,0:50:.:.:.:.:.:50 0|0:50,0:50:.:.:.:.:.:50 0|0:50,0:50:.:.:.:.:.:50
100
- 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|930561|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|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|930561|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|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|930561|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|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|930561|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|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|930561|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|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|930561|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|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|930561|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|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|930561|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|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|930561|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp| GT:AD:DP:VI:VIC:VID:VIG:VIM:GQ 1|1:0,50:50:AR:.:1:123016:1:50 1|0:25,25:50:.:.:.:.:.:50 0|0:50,0:50:.:.:.:.:.:50 0|0:50,0:50:.:.:.:.:.:50 0|0:50,0:50:.:.:.:.:.:50 0|0:50,0:50:.:.:.:.:.:50
100
+ 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|930561|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|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|930561|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|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|930561|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|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|930561|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|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|930561|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|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|930561|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|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|930561|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|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|930561|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|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|930561|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp| GT:AD:DP:VI:VIC:VID:VIG:VIM:GQ 1|1:0,50:50:.:.:.:.:.: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 0|0:50,0:50:.:.:.:.:.:50
101
101
  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:GQ 1|1:0,50:50:AR:.:1:0:50 0|0:50,0:50:.:.:.:.:50 1|0:45,5:50:.:.:.:.:50 0|0:50,0:50:.:.:.:.:50 1|0:25,25:50:.:.:.:.:50 0|0:50,0:50:.:.:.:.:50
102
102
  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:GQ 1|1:0,50:50:.:1:0:50 1|1:0,50:50:.:.:.:50 0|0:50,0:50:.:.:.:50 1|0:25,25:50:.:.:.:50 0|0:50,0:50:.:.:.:50 1|0:25,25:50:.:.:.:50
103
103
  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|||||||457686|Pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|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|||||||457686|Pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp| GT:AD:DP:VI:VIC:VID:VIM:GQ 1|1:0,50:50:AR:.:1:0 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
package/src/views/SampleVariants.tsx CHANGED
@@ -98,9 +98,19 @@ export const SampleVariants: Component<{
98
98
  actions.setSampleVariantsFilterQuery(
99
99
  props.sample,
100
100
  {
101
- selector: selectorVim,
102
- operator: "==",
103
- args: 1,
101
+ operator: "or",
102
+ args: [
103
+ {
104
+ selector: selectorVim,
105
+ operator: "==",
106
+ args: 1,
107
+ },
108
+ {
109
+ selector: selectorVim,
110
+ operator: "==",
111
+ args: null,
112
+ },
113
+ ],
104
114
  },
105
115
  selectorKey(selectorVim)
106
116
  );