@molgenis/vip-report-template 7.0.2 → 7.0.4

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 (9) hide show
  1. package/package.json +1 -1
  2. package/src/components/RecordsTable.tsx +2 -2
  3. package/src/components/VariantConsequenceContainer.tsx +5 -11
  4. package/src/components/VariantConsequenceTable.tsx +33 -42
  5. package/src/components/VariantContainer.tsx +4 -12
  6. package/src/components/VariantInfoTable.tsx +26 -15
  7. package/src/mocks/GRCh37/field_metadata.json +3 -3
  8. package/src/mocks/GRCh37/vcf/family.vcf.blob +7 -7
  9. package/src/mocks/GRCh38/field_metadata.json +21 -8
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@molgenis/vip-report-template",
3
- "version": "7.0.2",
3
+ "version": "7.0.4",
4
4
  "description": "Report Template for Variant Call Format (VCF) Report Generator",
5
5
  "license": "LGPL-3.0",
6
6
  "devDependencies": {
package/src/components/RecordsTable.tsx CHANGED
@@ -49,7 +49,7 @@ export const RecordsTableHeaderCells: Component<{ fieldConfigs: ConfigCells }> =
49
49
  );
50
50
  };
51
51
 
52
- const RecordsTableHeaderCell: Component<{
52
+ export const RecordsTableHeaderCell: Component<{
53
53
  fieldConfig: ConfigCellItem;
54
54
  }> = (props) => {
55
55
  const label = () => props.fieldConfig.label();
@@ -113,7 +113,7 @@ export const RecordsTableCell: Component<{
113
113
  );
114
114
  };
115
115
 
116
- const RecordsTableCellLine: Component<{
116
+ export const RecordsTableCellLine: Component<{
117
117
  fieldConfig: ConfigCellItem;
118
118
  record: Item<VcfRecord>;
119
119
  valueIndex: number;
package/src/components/VariantConsequenceContainer.tsx CHANGED
@@ -1,6 +1,6 @@
1
1
  import { Component, Show } from "solid-js";
2
2
  import { MetadataContainer, SampleContainer } from "../utils/api.ts";
3
- import { Value, VcfRecord } from "@molgenis/vip-report-vcf";
3
+ import { VcfRecord } from "@molgenis/vip-report-vcf";
4
4
  import { DecisionTree, Item, Sample } from "@molgenis/vip-report-api";
5
5
  import { VariantInfoTable } from "./VariantInfoTable.tsx";
6
6
  import { VariantConsequenceTable } from "./VariantConsequenceTable.tsx";
@@ -9,8 +9,6 @@ import { DecisionTreePath } from "./tree/DecisionTreePath.tsx";
9
9
  import { getDecisionTreePath, getSampleTreePath } from "../utils/decisionTree.ts";
10
10
  import { VariantType } from "../utils/variantType.ts";
11
11
  import { getPedigreeSamples } from "../utils/sample.ts";
12
- import { getInfoField, getInfoValue } from "../utils/vcf.ts";
13
- import { RuntimeError } from "../utils/error.ts";
14
12
  import { ConfigJson } from "../types/config";
15
13
  import { VariantGenotypeTable } from "./VariantGenotypeTable.tsx";
16
14
  import { initConfig } from "../utils/config/config.ts";
@@ -28,11 +26,6 @@ export const VariantConsequenceContainer: Component<{
28
26
  const config = () => initConfig(props.config, props.variantType, props.metadata, props.sample);
29
27
 
30
28
  const samples = (): Item<Sample>[] => (props.sample ? getPedigreeSamples(props.sample) : []);
31
- const csqField = () => {
32
- const csqField = getInfoField(props.metadata.records, "CSQ");
33
- if (csqField === undefined) throw new RuntimeError();
34
- return csqField;
35
- };
36
29
  const hasDecisionTreePathMeta = () =>
37
30
  (props.metadata.records.info.CSQ?.nested?.items || []).findIndex((csq) => csq.id === "VIPP") !== -1;
38
31
  const hasSampleTreePathMeta = () => props.metadata.records.format.VIPP_S != null;
@@ -43,14 +36,15 @@ export const VariantConsequenceContainer: Component<{
43
36
  <div class="column is-4">
44
37
  <div>
45
38
  <h1 class="title is-5">Info</h1>
46
- <VariantInfoTable infoMetadataContainer={props.metadata.records.info} infoContainer={props.record.data.n} />
39
+ <VariantInfoTable variantType={props.variantType} metadata={props.metadata} record={props.record} />
47
40
  </div>
48
41
  <div class="mt-3">
49
42
  <h1 class="title is-5">Consequence</h1>
50
43
  <VariantConsequenceTable
51
- csqMetadata={csqField().nested?.items || []}
52
- csqValues={(getInfoValue(props.record, 0, csqField()) as Value[])[props.consequenceId] as Value[]}
44
+ variantType={props.variantType}
45
+ metadata={props.metadata}
53
46
  record={props.record}
47
+ consequenceId={props.consequenceId}
54
48
  />
55
49
  </div>
56
50
  <div class="mt-3">
package/src/components/VariantConsequenceTable.tsx CHANGED
@@ -1,58 +1,49 @@
1
- import { Component, createMemo, For, Show } from "solid-js";
2
- import { FieldMetadata, ValueArray, VcfRecord } from "@molgenis/vip-report-vcf";
1
+ import { Component, For } from "solid-js";
2
+ import { VcfRecord } from "@molgenis/vip-report-vcf";
3
3
  import { Item } from "@molgenis/vip-report-api";
4
- import { FieldTyped } from "./field/typed/FieldTyped.tsx";
5
4
  import { Table } from "./Table.tsx";
6
- import { abbreviateHeader } from "../utils/utils.ts";
5
+ import { initConfigCells } from "../utils/config/configCells.ts";
6
+ import { RecordsTableCellLine, RecordsTableHeaderCell } from "./RecordsTable.tsx";
7
+ import { VariantType } from "../utils/variantType.ts";
8
+ import { MetadataContainer } from "../utils/api.ts";
7
9
 
8
10
  export const VariantConsequenceTable: Component<{
9
- csqMetadata: FieldMetadata[];
10
- csqValues: ValueArray;
11
+ variantType: VariantType;
12
+ metadata: MetadataContainer;
11
13
  record: Item<VcfRecord>;
14
+ consequenceId: number;
12
15
  }> = (props) => {
13
- function getValues(index: number): ValueArray {
14
- return props.csqValues[index] !== null ? (props.csqValues[index] as ValueArray) : [];
15
- }
16
+ const configCells = () =>
17
+ initConfigCells(
18
+ [
19
+ {
20
+ type: "info",
21
+ name: "CSQ/.*",
22
+ },
23
+ ],
24
+ props.variantType,
25
+ props.metadata,
26
+ null,
27
+ ).filter((configCell) => configCell.type !== "group");
16
28
 
17
29
  return (
18
30
  <Table borderless={true}>
19
31
  <tbody>
20
- <For each={props.csqMetadata}>
21
- {(field: FieldMetadata, index) => (
22
- <Show when={!(getValues(index()).length === 0)}>
23
- <tr>
24
- <FieldHeader field={field} />
25
- <td>
26
- <FieldTyped metadata={field} value={props.csqValues[index()]} />
27
- </td>
28
- </tr>
29
- </Show>
32
+ <For each={configCells()}>
33
+ {(fieldConfig) => (
34
+ <tr>
35
+ <RecordsTableHeaderCell fieldConfig={fieldConfig} />
36
+ <td>
37
+ <RecordsTableCellLine
38
+ fieldConfig={fieldConfig}
39
+ record={props.record}
40
+ valueIndex={props.consequenceId}
41
+ />
42
+ </td>
43
+ </tr>
30
44
  )}
31
45
  </For>
32
46
  </tbody>
33
47
  </Table>
34
48
  );
35
49
  };
36
-
37
- const FieldHeader: Component<{
38
- field: FieldMetadata;
39
- vertical?: boolean;
40
- rowspan?: number;
41
- colspan?: number;
42
- }> = (props) => {
43
- const label = createMemo(() => abbreviateHeader(props.field.label || props.field.id));
44
- return (
45
- <th
46
- style={props.vertical ? { "writing-mode": "vertical-rl" } : undefined}
47
- rowspan={props.rowspan}
48
- colspan={props.colspan}
49
- >
50
- <Show
51
- when={props.field.description && props.field.description !== label()}
52
- fallback={<abbr title={props.field.label || props.field.id}>{label()}</abbr>}
53
- >
54
- <abbr title={props.field.description}>{label()}</abbr>
55
- </Show>
56
- </th>
57
- );
58
- };
package/src/components/VariantContainer.tsx CHANGED
@@ -34,18 +34,10 @@ export const VariantContainer: Component<{
34
34
  <h1 class="title is-5">Record</h1>
35
35
  <VariantTable variant={props.record.data} />
36
36
  </div>
37
- <Show
38
- when={
39
- Object.values(props.metadata.records.info).filter(
40
- (info) => !info.nested && props.record.data.n[info.id] !== undefined,
41
- ).length > 0
42
- }
43
- >
44
- <div class="column is-3">
45
- <h1 class="title is-5">Info</h1>
46
- <VariantInfoTable infoMetadataContainer={props.metadata.records.info} infoContainer={props.record.data.n} />
47
- </div>
48
- </Show>
37
+ <div class="column is-3">
38
+ <h1 class="title is-5">Info</h1>
39
+ <VariantInfoTable variantType={props.variantType} metadata={props.metadata} record={props.record} />
40
+ </div>
49
41
  <Show when={config().variant.samplesCells}>
50
42
  {(samplesCells) => (
51
43
  <div class="column">
package/src/components/VariantInfoTable.tsx CHANGED
@@ -1,27 +1,38 @@
1
1
  import { Component, For } from "solid-js";
2
- import { FieldMetadataContainer, InfoContainer } from "@molgenis/vip-report-vcf";
3
- import { FieldInfo } from "./field/info/FieldInfo.tsx";
2
+ import { VcfRecord } from "@molgenis/vip-report-vcf";
4
3
  import { Table } from "./Table.tsx";
4
+ import { Item } from "@molgenis/vip-report-api";
5
+ import { RecordsTableCell, RecordsTableHeaderCell } from "./RecordsTable.tsx";
6
+ import { initConfigCells } from "../utils/config/configCells.ts";
7
+ import { MetadataContainer } from "../utils/api.ts";
8
+ import { VariantType } from "../utils/variantType.ts";
5
9
 
6
10
  export const VariantInfoTable: Component<{
7
- infoMetadataContainer: FieldMetadataContainer;
8
- infoContainer: InfoContainer;
11
+ variantType: VariantType;
12
+ metadata: MetadataContainer;
13
+ record: Item<VcfRecord>;
9
14
  }> = (props) => {
10
- const fieldMetadatas = () =>
11
- Object.values(props.infoMetadataContainer).filter(
12
- (info) => !info.nested && props.infoContainer[info.id] !== undefined,
13
- );
15
+ const configCells = () =>
16
+ initConfigCells(
17
+ [
18
+ {
19
+ type: "info",
20
+ name: "((?!CSQ).)*",
21
+ },
22
+ ],
23
+ props.variantType,
24
+ props.metadata,
25
+ null,
26
+ ).filter((configCell) => configCell.type !== "group");
14
27
 
15
28
  return (
16
- <Table>
29
+ <Table borderless={true}>
17
30
  <tbody>
18
- <For each={fieldMetadatas()}>
19
- {(fieldMetadata) => (
31
+ <For each={configCells()}>
32
+ {(fieldConfig) => (
20
33
  <tr>
21
- <td>{fieldMetadata.id}</td>
22
- <td>
23
- <FieldInfo metadata={fieldMetadata} value={props.infoContainer[fieldMetadata.id]} />
24
- </td>
34
+ <RecordsTableHeaderCell fieldConfig={fieldConfig} />
35
+ <RecordsTableCell fieldConfig={fieldConfig} record={props.record} />
25
36
  </tr>
26
37
  )}
27
38
  </For>
package/src/mocks/GRCh37/field_metadata.json CHANGED
@@ -180,7 +180,7 @@
180
180
  "label": "ClinVar",
181
181
  "description": "Clinical significance for this single variant",
182
182
  "numberType": "OTHER",
183
- "separator": "/",
183
+ "separator": "&",
184
184
  "type": "CATEGORICAL",
185
185
  "categories": {
186
186
  "Benign": {
@@ -765,8 +765,8 @@
765
765
  "STR_STATUS": {
766
766
  "label": "STR status",
767
767
  "description": "Repeat expansion status as decided by Stranger",
768
- "numberType": "NUMBER",
769
- "numberCount": 1,
768
+ "numberType": "PER_ALT",
769
+ "separator": ",",
770
770
  "type": "CATEGORICAL",
771
771
  "categories": {
772
772
  "normal": {
package/src/mocks/GRCh37/vcf/family.vcf.blob CHANGED
@@ -105,21 +105,21 @@
105
105
  1 10042538 . C T . PASS CSQ=T|missense_variant|MODERATE|NMNAT1|64802|Transcript|NM_001297778.1|protein_coding|5/5||NM_001297778.1:c.619C>T|NP_001284707.1:p.Arg207Trp|778/3796|619/840|207/279|R/W|Cgg/Tgg|rs142968179&CM127756|1||1||1|EntrezGene|||||0.04|0.08||pathogenic||1&1|26103963&22842229&22842230|||||||101|0|-36|-16|17|0.00|0.00|0.00|0.00|NMNAT1|VUS|0.13080463||||||||1.09||AR||LP||||3.917000|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|0.12802194||||||||1.09||AR||LP||||3.917000|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|||||||101|0|-36|-16|17|0.00|0.00|0.00|0.00|NMNAT1|VUS|0.14871566||||||||1.09||AR||LP||||3.917000|1:10042538-10042538|3.88948e-05|0|37133|Pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp;VIPC_S=LQ GT:AD:DP:GQ:VI:VID:VIG:VIM:VIPC_S:VIPP_S 1|1:0,50:50:10:AR:1:64802:1:U3,U3,U3:GQ&exit_u3,GQ&exit_u3,GQ&exit_u3 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:.:.:.:.:.:.
106
106
  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|0.032756623||||||HP:0000951||1.439||AR||LP||||-0.860000|1:16375584-16375585|0.000548455|0|638508|Pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|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|0.9124473||||||HP:0000951||1.439||AR||LP||||-0.860000|1:16375584-16375585|0.000548455|0|638508|Pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp,-|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000001994|promoter||||||||||rs751608665|1|||||||||||||uncertain_significance&pathogenic||1|||||||||||||||||||||||||||||||||||-0.860000|1:16375584-16375585|0.000548455|0|638508|Pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LQ|exit_rm,-|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000922299|CTCF_binding_site||||||||||rs751608665|1|||||||||||||uncertain_significance&pathogenic||1|||||||||||||||||||||||||||||||||||-0.860000|1:16375584-16375585|0.000548455|0|638508|Pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LQ|exit_rm,-|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00533524886|||||||||||rs751608665|1||1|||||||||||uncertain_significance&pathogenic||1|||ENSPFM0617|1|N||ZBTB7B&ZBTB7A&ZBTB7C||||||||||||||||||||||||||||-0.860000|1:16375584-16375585|0.000548455|0|638508|Pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LQ|exit_rm,-|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00529659450|||||||||||rs751608665|1||1|||||||||||uncertain_significance&pathogenic||1|||ENSPFM0566|3|N||TEAD4::MAX||||||||||||||||||||||||||||-0.860000|1:16375584-16375585|0.000548455|0|638508|Pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LQ|exit_rm,-|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00529435523|||||||||||rs751608665|1||1|||||||||||uncertain_significance&pathogenic||1|||ENSPFM0544|3|N||TEAD4::FIGLA||||||||||||||||||||||||||||-0.860000|1:16375584-16375585|0.000548455|0|638508|Pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LQ|exit_rm,-|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00910553844|||||||||||rs751608665|1||1|||||||||||uncertain_significance&pathogenic||1|||ENSPFM0383|17|N||MGA::EVX1||||||||||||||||||||||||||||-0.860000|1:16375584-16375585|0.000548455|0|638508|Pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LQ|exit_rm;VIPC_S=OK GT:AD:DP:GQ:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S:VIS 1|0:25,25:50:50:AR:1_16376412_G_A,1_16376412_G_N:0:1188:1:OK,OK,OK,OK,OK,OK,OK,OK:GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1:AR_C 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:.:.:.:.:.:.:.:.
107
107
  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|0.9316635||||||HP:0000951||1.439||AR||||||4.909000||||||||LP|filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&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|0.9316635||||||HP:0000951||1.439||AR||||||4.909000||||||||LP|filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp;VIPC_S=OK GT:AD:DP:GQ:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S:VIS 1|0:5,45:50:.:AR_C,AD:1_16376412_G_A,1_16375583_GA_G:1:1188:1:OK,OK:GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1: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:.:.:.:.:.:.:.:.
108
- 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|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|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:GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1: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:.:.:.:.:.:.:.:.
109
- 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|filter&vkgl&exit_lp;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIG:VIM:VIPC_S:VIPP_S 1|1:0,50:19:19:AR:1:6390:1:OK:GQ&DP&VIM&exit_u1 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:.:.:.:.:.:.
108
+ 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|Likely_pathogenic||no_assertion_criteria_provided|LP|filter&vkgl&exit_lp,A|splice_donor_variant|HIGH|CLCNKB|1188|Transcript|NM_001165945.2|protein_coding||3/12|NM_001165945.2:c.461+1G>A|||||||rs201204502&CS1211892&CS971662|1||1|||EntrezGene||||||||||0&1&1|||||||||17|-36|-28|-1|0.00|0.00|0.03|0.97|CLCNKB|VUS|0.9882061||||||HP:0000951||1.439||AR||LP||||4.909000|1:16376412-16376412|6.38086e-05|0|1285112|Likely_pathogenic||no_assertion_criteria_provided|LP|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:GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1: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:.:.:.:.:.:.:.:.
109
+ 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|Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIG:VIM:VIPC_S:VIPP_S 1|1:0,50:19:19:AR:1:6390:1:OK:GQ&DP&VIM&exit_u1 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:.:.:.:.:.:.
110
110
  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|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:GQ&DP&VIM&exit_u1 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:.:.:.:.:.:.
111
111
  1 152520788 symbolic1 A <DEL> . PASS CSQ=deletion|transcript_ablation|HIGH|LCE3D|84648|Transcript|NM_032563.2|protein_coding|||||||||||1||-1||1|EntrezGene|||||||||||||||||||||||||||||||||||||||||||||||||||||VUS|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|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|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|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|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|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|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|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|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|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|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|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|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|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|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:GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1:123456_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:.:.:.:.:.
112
112
  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|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:GQ&DP&VIM&VID&exit_u1 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:.:.:.:.:.:.
113
113
  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|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|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|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|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|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|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|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|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|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|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|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|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|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|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|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|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|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|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|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|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|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|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|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|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|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|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:GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1 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:.:.:.:.:.:.
114
- 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|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|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|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|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|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:.:GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1 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:.:.:.:.:.:.
114
+ 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|Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|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|||||||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|Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|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|||||||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|Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|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|||||||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|Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|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||||||||||||||||||||||||||||||||||9.359000|4:106320294-106320294|0.000211803|0|372226|Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LQ|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:.:GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1 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:.:.:.:.:.:.
115
115
  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|0.97944254|||||||LC|4.243||AD&AR||||||||||||||LP|filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIG:VIM:VIPC_S:VIPP_S 1|1:0,10:10:.:AR:0:19:1:OK:GQ&DP&VIM&exit_u1 0|1:1,49:50:50:.:.:.:.:.:. 1|0:0,50:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.
116
116
  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|0.998016||||||HP:0000951|LC|4.243||AD&AR||LP||||4.010000||||||||LP|filter&vkgl&exit_lp;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIG:VIM:VIPC_S:VIPP_S 1|0:10,90:50:50:AD:1:19:1:OK:GQ&DP&VIM&exit_u1 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:.:.:.:.:.:.
117
117
  9 107584865 . C G . 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|0.998016||||||HP:0003124|HC|4.243||AD&AR||LP||||4.010000||||||||LP|filter&vkgl&exit_lp;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIG:VIM:VIPC_S:VIPP_S 1|0:10,90:50:50:AD:1:19:1:OK:GQ&DP&VIM&exit_u1 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:.:.:.:.:.:.
118
- 10 126091499 . G C . PASS CSQ=C|stop_gained|HIGH|OAT|4942|Transcript|NM_000274.4|protein_coding|7/10||NM_000274.4:c.897C>G|NP_000265.1:p.Tyr299Ter|977/2039|897/1320|299/439|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808||||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.9327103||||||||-1.183||AR||LP||||1.254000|10:126091499-126091499|1.59133e-05|0|176|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001171814.2|protein_coding|6/9||NM_001171814.2:c.483C>G|NP_001165285.1:p.Tyr161Ter|749/1811|483/906|161/301|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808||||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.98210585||||||||-1.183||AR||LP||||1.254000|10:126091499-126091499|1.59133e-05|0|176|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322965.2|protein_coding|7/10||NM_001322965.2:c.897C>G|NP_001309894.1:p.Tyr299Ter|972/2034|897/1320|299/439|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808||||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.9327103||||||||-1.183||AR||LP||||1.254000|10:126091499-126091499|1.59133e-05|0|176|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322966.2|protein_coding|8/11||NM_001322966.2:c.897C>G|NP_001309895.1:p.Tyr299Ter|1292/2354|897/1320|299/439|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1||1|EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808||||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.97306395||||||||-1.183||AR||LP||||1.254000|10:126091499-126091499|1.59133e-05|0|176|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322967.2|protein_coding|8/11||NM_001322967.2:c.897C>G|NP_001309896.1:p.Tyr299Ter|1097/2159|897/1320|299/439|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808||||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.9656282||||||||-1.183||AR||LP||||1.254000|10:126091499-126091499|1.59133e-05|0|176|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322968.2|protein_coding|9/12||NM_001322968.2:c.897C>G|NP_001309897.1:p.Tyr299Ter|1184/2246|897/1320|299/439|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808||||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.96872944||||||||-1.183||AR||LP||||1.254000|10:126091499-126091499|1.59133e-05|0|176|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322969.2|protein_coding|8/11||NM_001322969.2:c.897C>G|NP_001309898.1:p.Tyr299Ter|1064/2126|897/1320|299/439|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808||||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.9635119||||||||-1.183||AR||LP||||1.254000|10:126091499-126091499|1.59133e-05|0|176|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322970.2|protein_coding|9/12||NM_001322970.2:c.897C>G|NP_001309899.1:p.Tyr299Ter|1280/2342|897/1320|299/439|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808||||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.97306395||||||||-1.183||AR||LP||||1.254000|10:126091499-126091499|1.59133e-05|0|176|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322971.2|protein_coding|5/8||NM_001322971.2:c.576C>G|NP_001309900.1:p.Tyr192Ter|656/1718|576/999|192/332|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808||||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.96748227||||||||-1.183||AR||LP||||1.254000|10:126091499-126091499|1.59133e-05|0|176|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322974.2|protein_coding|7/10||NM_001322974.2:c.297C>G|NP_001309903.1:p.Tyr99Ter|863/1925|297/720|99/239|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808||||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.96553046||||||||-1.183||AR||LP||||1.254000|10:126091499-126091499|1.59133e-05|0|176|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|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:1:4942:1:OK,OK,OK,OK,OK,OK,OK,OK,OK,OK:GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1 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:.:.:.:.:.:.
118
+ 10 126091499 . G C . PASS CSQ=C|stop_gained|HIGH|OAT|4942|Transcript|NM_000274.4|protein_coding|7/10||NM_000274.4:c.897C>G|NP_000265.1:p.Tyr299Ter|977/2039|897/1320|299/439|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808||||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.9327103||||||||-1.183||AR||LP||||1.254000|10:126091499-126091499|1.59133e-05|0|176|Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001171814.2|protein_coding|6/9||NM_001171814.2:c.483C>G|NP_001165285.1:p.Tyr161Ter|749/1811|483/906|161/301|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808||||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.98210585||||||||-1.183||AR||LP||||1.254000|10:126091499-126091499|1.59133e-05|0|176|Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322965.2|protein_coding|7/10||NM_001322965.2:c.897C>G|NP_001309894.1:p.Tyr299Ter|972/2034|897/1320|299/439|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808||||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.9327103||||||||-1.183||AR||LP||||1.254000|10:126091499-126091499|1.59133e-05|0|176|Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322966.2|protein_coding|8/11||NM_001322966.2:c.897C>G|NP_001309895.1:p.Tyr299Ter|1292/2354|897/1320|299/439|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1||1|EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808||||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.97306395||||||||-1.183||AR||LP||||1.254000|10:126091499-126091499|1.59133e-05|0|176|Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322967.2|protein_coding|8/11||NM_001322967.2:c.897C>G|NP_001309896.1:p.Tyr299Ter|1097/2159|897/1320|299/439|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808||||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.9656282||||||||-1.183||AR||LP||||1.254000|10:126091499-126091499|1.59133e-05|0|176|Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322968.2|protein_coding|9/12||NM_001322968.2:c.897C>G|NP_001309897.1:p.Tyr299Ter|1184/2246|897/1320|299/439|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808||||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.96872944||||||||-1.183||AR||LP||||1.254000|10:126091499-126091499|1.59133e-05|0|176|Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322969.2|protein_coding|8/11||NM_001322969.2:c.897C>G|NP_001309898.1:p.Tyr299Ter|1064/2126|897/1320|299/439|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808||||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.9635119||||||||-1.183||AR||LP||||1.254000|10:126091499-126091499|1.59133e-05|0|176|Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322970.2|protein_coding|9/12||NM_001322970.2:c.897C>G|NP_001309899.1:p.Tyr299Ter|1280/2342|897/1320|299/439|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808||||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.97306395||||||||-1.183||AR||LP||||1.254000|10:126091499-126091499|1.59133e-05|0|176|Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322971.2|protein_coding|5/8||NM_001322971.2:c.576C>G|NP_001309900.1:p.Tyr192Ter|656/1718|576/999|192/332|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808||||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.96748227||||||||-1.183||AR||LP||||1.254000|10:126091499-126091499|1.59133e-05|0|176|Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322974.2|protein_coding|7/10||NM_001322974.2:c.297C>G|NP_001309903.1:p.Tyr99Ter|863/1925|297/720|99/239|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808||||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.96553046||||||||-1.183||AR||LP||||1.254000|10:126091499-126091499|1.59133e-05|0|176|Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|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:1:4942:1:OK,OK,OK,OK,OK,OK,OK,OK,OK,OK:GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1 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:.:.:.:.:.:.
119
119
  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||||||||194|-27|-43|-27|-1|0.00|0.00|0.01|0.00|CLN5|VUS|0.9957157||||||||1.166||AR||LP||||9.873000||||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||||||||194|-27|-43|-27|-1|0.00|0.00|0.01|0.00|CLN5|VUS|0.99436617||||||||1.166||AR||LP||||9.873000||||623394|Pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp;VIPC_S=OK GT:AD:DP:GQ:VID:VIM:VIPC_S:VIPP_S 1|1:0,50:50:50:1:0:OK,OK:GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1 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:.:.:.:.
120
- 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|0.9826843||||||HP:0000951||1.263||AR||LP||||3.737000|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|0.007844023|0|1|17|uSTOP_gained_Evidence:False&uSTOP_gained_KozakContext:GCCATGA&uSTOP_gained_KozakStrength:Moderate&uSTOP_gained_newSTOPDistanceToCDS:34&uSTOP_gained_ref_StartDistanceToCDS:562&uSTOP_gained_ref_type:uORF&uSTOP_gained_Evidence:False&uSTOP_gained_KozakContext:GAGATGG&uSTOP_gained_KozakStrength:Strong&uSTOP_gained_newSTOPDistanceToCDS:34&uSTOP_gained_ref_StartDistanceToCDS:550&uSTOP_gained_ref_type:uORF&uSTOP_gained_Evidence:False&uSTOP_gained_KozakContext:CAGATGC&uSTOP_gained_KozakStrength:Weak&uSTOP_gained_newSTOPDistanceToCDS:34&uSTOP_gained_ref_StartDistanceToCDS:475&uSTOP_gained_ref_type:uORF&uSTOP_gained_Evidence:False&uSTOP_gained_KozakContext:GAAATGG&uSTOP_gained_KozakStrength:Strong&uSTOP_gained_newSTOPDistanceToCDS:34&uSTOP_gained_ref_StartDistanceToCDS:412&uSTOP_gained_ref_type:uORF&uSTOP_gained_Evidence:False&uSTOP_gained_KozakContext:GAAATGA&uSTOP_gained_KozakStrength:Moderate&uSTOP_gained_newSTOPDistanceToCDS:34&uSTOP_gained_ref_StartDistanceToCDS:364&uSTOP_gained_ref_type:uORF&uSTOP_gained_Evidence:False&uSTOP_gained_KozakContext:ATGATGC&uSTOP_gained_KozakStrength:Moderate&uSTOP_gained_newSTOPDistanceToCDS:34&uSTOP_gained_ref_StartDistanceToCDS:361&uSTOP_gained_ref_type:uORF&uSTOP_gained_Evidence:False&uSTOP_gained_KozakContext:ACTATGG&uSTOP_gained_KozakStrength:Strong&uSTOP_gained_newSTOPDistanceToCDS:34&uSTOP_gained_ref_StartDistanceToCDS:190&uSTOP_gained_ref_type:uORF&uSTOP_gained_Evidence:False&uSTOP_gained_KozakContext:TCCATGC&uSTOP_gained_KozakStrength:Weak&uSTOP_gained_newSTOPDistanceToCDS:34&uSTOP_gained_ref_StartDistanceToCDS:97&uSTOP_gained_ref_type:uORF|uSTOP_gained&uSTOP_gained&uSTOP_gained&uSTOP_gained&uSTOP_gained&uSTOP_gained&uSTOP_gained&uSTOP_gained|HP:0000951||1.263||AR||LP||||3.737000|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|0.065462574||||||HP:0000951||1.263||AR||LP||||3.737000|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|0.9942367||||||HP:0000951||1.263||AR||LP||||3.737000|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|0.065462574||||||HP:0000951||1.263||AR||LP||||3.737000|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|0.9777649||||||HP:0000951||1.263||AR||LP||||3.737000|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|0.9769935||||||HP:0000951||1.263||AR||LP||||3.737000|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|0.065462574||||||HP:0000951||1.263||AR||LP||||3.737000|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|0.0989985||||||HP:0000951||1.263||AR||LP||||3.737000|14:89307838-89307838|3.99307e-06|0|997900|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp,T|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001864166|enhancer||||||||||rs376035653|1||||||||||||||||||||||||||||||||||||||||||||||||||3.737000|14:89307838-89307838|3.99307e-06|0|997900|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LQ|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,OK,OK,OK,OK:GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1 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:.:.:.:.:.
120
+ 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|0.9826843||||||HP:0000951||1.263||AR||LP||||3.737000|14:89307838-89307838|3.99307e-06|0|997900|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|0.007844023|0|1|17|uSTOP_gained_Evidence:False&uSTOP_gained_KozakContext:GCCATGA&uSTOP_gained_KozakStrength:Moderate&uSTOP_gained_newSTOPDistanceToCDS:34&uSTOP_gained_ref_StartDistanceToCDS:562&uSTOP_gained_ref_type:uORF&uSTOP_gained_Evidence:False&uSTOP_gained_KozakContext:GAGATGG&uSTOP_gained_KozakStrength:Strong&uSTOP_gained_newSTOPDistanceToCDS:34&uSTOP_gained_ref_StartDistanceToCDS:550&uSTOP_gained_ref_type:uORF&uSTOP_gained_Evidence:False&uSTOP_gained_KozakContext:CAGATGC&uSTOP_gained_KozakStrength:Weak&uSTOP_gained_newSTOPDistanceToCDS:34&uSTOP_gained_ref_StartDistanceToCDS:475&uSTOP_gained_ref_type:uORF&uSTOP_gained_Evidence:False&uSTOP_gained_KozakContext:GAAATGG&uSTOP_gained_KozakStrength:Strong&uSTOP_gained_newSTOPDistanceToCDS:34&uSTOP_gained_ref_StartDistanceToCDS:412&uSTOP_gained_ref_type:uORF&uSTOP_gained_Evidence:False&uSTOP_gained_KozakContext:GAAATGA&uSTOP_gained_KozakStrength:Moderate&uSTOP_gained_newSTOPDistanceToCDS:34&uSTOP_gained_ref_StartDistanceToCDS:364&uSTOP_gained_ref_type:uORF&uSTOP_gained_Evidence:False&uSTOP_gained_KozakContext:ATGATGC&uSTOP_gained_KozakStrength:Moderate&uSTOP_gained_newSTOPDistanceToCDS:34&uSTOP_gained_ref_StartDistanceToCDS:361&uSTOP_gained_ref_type:uORF&uSTOP_gained_Evidence:False&uSTOP_gained_KozakContext:ACTATGG&uSTOP_gained_KozakStrength:Strong&uSTOP_gained_newSTOPDistanceToCDS:34&uSTOP_gained_ref_StartDistanceToCDS:190&uSTOP_gained_ref_type:uORF&uSTOP_gained_Evidence:False&uSTOP_gained_KozakContext:TCCATGC&uSTOP_gained_KozakStrength:Weak&uSTOP_gained_newSTOPDistanceToCDS:34&uSTOP_gained_ref_StartDistanceToCDS:97&uSTOP_gained_ref_type:uORF|uSTOP_gained&uSTOP_gained&uSTOP_gained&uSTOP_gained&uSTOP_gained&uSTOP_gained&uSTOP_gained&uSTOP_gained|HP:0000951||1.263||AR||LP||||3.737000|14:89307838-89307838|3.99307e-06|0|997900|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|0.065462574||||||HP:0000951||1.263||AR||LP||||3.737000|14:89307838-89307838|3.99307e-06|0|997900|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|0.9942367||||||HP:0000951||1.263||AR||LP||||3.737000|14:89307838-89307838|3.99307e-06|0|997900|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|0.065462574||||||HP:0000951||1.263||AR||LP||||3.737000|14:89307838-89307838|3.99307e-06|0|997900|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|0.9777649||||||HP:0000951||1.263||AR||LP||||3.737000|14:89307838-89307838|3.99307e-06|0|997900|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|0.9769935||||||HP:0000951||1.263||AR||LP||||3.737000|14:89307838-89307838|3.99307e-06|0|997900|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|0.065462574||||||HP:0000951||1.263||AR||LP||||3.737000|14:89307838-89307838|3.99307e-06|0|997900|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|0.0989985||||||HP:0000951||1.263||AR||LP||||3.737000|14:89307838-89307838|3.99307e-06|0|997900|Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp,T|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001864166|enhancer||||||||||rs376035653|1||||||||||||||||||||||||||||||||||||||||||||||||||3.737000|14:89307838-89307838|3.99307e-06|0|997900|Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LQ|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,OK,OK,OK,OK:GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1 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:.:.:.:.:.
121
121
  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|0.9902351||||||HP:0000951||1.263||AR||LP||||8.399000||||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|0.8040881||||||HP:0000951||1.263||AR||LP||||8.399000||||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|0.9902351||||||HP:0000951||1.263||AR||LP||||8.399000||||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|0.9902351||||||HP:0000951||1.263||AR||LP||||8.399000||||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|0.9902351||||||HP:0000951||1.263||AR||LP||||8.399000||||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|0.9902351||||||HP:0000951||1.263||AR||LP||||8.399000||||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|0.9902351||||||HP:0000951||1.263||AR||LP||||8.399000||||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|0.9902351||||||HP:0000951||1.263||AR||LP||||8.399000||||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|0.9901416||||||HP:0000951||1.263||AR||LP||||8.399000||||2531|Pathogenic||no_assertion_criteria_provided|LP|filter&vkgl&exit_lp;VIPC_S=LQ GT:AD:DP:GQ:VI:VID:VIG:VIM:VIPC_S:VIPP_S 1|1:0,9:9:50:AR:0:123016:1:U3,U3,U3,U3,U3,U3,U3,U3,U3:GQ&DP&exit_u3,GQ&DP&exit_u3,GQ&DP&exit_u3,GQ&DP&exit_u3,GQ&DP&exit_u3,GQ&DP&exit_u3,GQ&DP&exit_u3,GQ&DP&exit_u3,GQ&DP&exit_u3 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:.:.:.:.:.:.
122
- 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|0.9979407||||||HP:0000951||1.263||AR||LP||||9.393000|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|0.9975501||||||HP:0000951||1.263||AR||LP||||9.393000|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|0.9940432||||||HP:0000951||1.263||AR||LP||||9.393000|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|0.99769527||||||HP:0000951||1.263||AR||LP||||9.393000|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|0.9988078||||||HP:0000951||1.263||AR||LP||||9.393000|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|0.99404776||||||HP:0000951||1.263||AR||LP||||9.393000|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|0.9971411||||||HP:0000951||1.263||AR||LP||||9.393000|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|0.9968329||||||HP:0000951||1.263||AR||LP||||9.393000|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|0.6298463||||||HP:0000951||1.263||AR||LP||||9.393000|14:89336408-89336409|1.19537e-05|0|930561|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|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:1:123016:1:OK,OK,OK,OK,OK,OK,OK,OK,OK:GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1 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:.:.:.:.:.:.
122
+ 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|0.9979407||||||HP:0000951||1.263||AR||LP||||9.393000|14:89336408-89336409|1.19537e-05|0|930561|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|0.9975501||||||HP:0000951||1.263||AR||LP||||9.393000|14:89336408-89336409|1.19537e-05|0|930561|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|0.9940432||||||HP:0000951||1.263||AR||LP||||9.393000|14:89336408-89336409|1.19537e-05|0|930561|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|0.99769527||||||HP:0000951||1.263||AR||LP||||9.393000|14:89336408-89336409|1.19537e-05|0|930561|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|0.9988078||||||HP:0000951||1.263||AR||LP||||9.393000|14:89336408-89336409|1.19537e-05|0|930561|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|0.99404776||||||HP:0000951||1.263||AR||LP||||9.393000|14:89336408-89336409|1.19537e-05|0|930561|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|0.9971411||||||HP:0000951||1.263||AR||LP||||9.393000|14:89336408-89336409|1.19537e-05|0|930561|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|0.9968329||||||HP:0000951||1.263||AR||LP||||9.393000|14:89336408-89336409|1.19537e-05|0|930561|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|0.6298463||||||HP:0000951||1.263||AR||LP||||9.393000|14:89336408-89336409|1.19537e-05|0|930561|Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|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:1:123016:1:OK,OK,OK,OK,OK,OK,OK,OK,OK:GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1 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:.:.:.:.:.:.
123
123
  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||||||||||||102|-28|-2|37|-2|0.00|0.00|0.00|0.00|INF2|VUS|0.9748948||||||||0.87||AD||LP||||7.817000||||||||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||||||||||||102|-28|-2|37|-2|0.00|0.00|0.00|0.00|INF2|VUS|0.97195035||||||||0.87||AD||LP||||7.817000||||||||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||||||||||||102|-28|-2|37|-2|0.00|0.00|0.00|0.00|INF2|VUS|0.97388726||||||||0.87||AD||LP||||7.817000||||||||LP|filter&vkgl&exit_lp,G|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001573054|open_chromatin_region|||||||||||1||||||||||||||||||||||||||||||||||||||||||||||||||7.817000||||||||LQ|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:GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1 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:.:.:.:.:.
124
124
  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|0.9992588||||||HP:0000951||0.583|1|AD||LP||||4.630000||||||||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|0.99961036||||||HP:0000951||0.583|1|AD||LP||||4.630000||||||||LP|filter&vkgl&exit_lp;VIPC_S=OK GT:AD:DP:GQ:VID:VIM:VIPC_S:VIPP_S 1|1:0,50:50:50:1:0:NOK,NOK:GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1 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:.:.:.:.
125
125
  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|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|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:GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1 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:.:.:.:.:.
@@ -129,6 +129,6 @@
129
129
  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|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|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|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|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|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|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:GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1 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:.:.:.:.:.
130
130
  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|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|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|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|filter&vkgl&exit_lp,-|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001610216|CTCF_binding_site|||||||||||1||||||||||||||||||||||||||||||||||||||||||||||||||5.586000||||||||LQ|exit_rm,-|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001909308|promoter|||||||||||1||||||||||||||||||||||||||||||||||||||||||||||||||5.586000||||||||LQ|exit_rm,-|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00523665928||||||||||||1||1||||||||||||||||ENSPFM0305|8|N||HOXB2::ELF1||||||||||||||||||||||||||||5.586000||||||||LQ|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:GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1,GQ&DP&VIM&exit_u1 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:.:.:.:.:.:.
131
131
  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|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|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|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|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|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|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|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|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|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|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|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|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|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|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|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|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|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|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|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|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|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|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|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|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|exit_rm;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIM:VIPC_S:VIPP_S 1|1:0,50:50:50:AR:.: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:GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1 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:.:.:.:.:.
132
- 22 51224051 . G A . PASS CSQ=A|missense_variant|MODERATE|FAKE|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|filter&vkgl&exit_lp;VIPC_S=OK GT:AD:VI:VID:VIG:VIM:VIPC_S:VIPP_S 1|1:0,50:AR:1:6390:1:OK:VIM&exit_u1 1|0:45,5:.:.:.:.:.:. 0|0:50,0:.:.:.:.:.:. 1|0:25,25:.:.:.:.:.:. 0|0:50,0:.:.:.:.:.:. 0|0:50,0:.:.:.:.:.:.
132
+ 22 51224051 . G A . PASS CSQ=A|missense_variant|MODERATE|FAKE|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|Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp;VIPC_S=OK GT:AD:VI:VID:VIG:VIM:VIPC_S:VIPP_S 1|1:0,50:AR:1:6390:1:OK:VIM&exit_u1 1|0:45,5:.:.:.:.:.:. 0|0:50,0:.:.:.:.:.:. 1|0:25,25:.:.:.:.:.:. 0|0:50,0:.:.:.:.:.:. 0|0:50,0:.:.:.:.:.:.
133
133
  X 48933021 x_chrom A T . PASS CSQ=T|splice_donor_variant|HIGH|WDR45|11152|Transcript|NM_001029896.2|protein_coding||9/10|NM_001029896.2:c.827+2T>A|||||||CS135341|1||-1|||EntrezGene||||||||||1|||||||||27|28|-2|2|0.02|0.00|0.01|0.99|WDR45|VUS|0.9742088||||||HP:0000951||1.088||XL||LP||||8.134000||||||||LP|filter&vkgl&exit_lp,T|splice_donor_variant|HIGH|WDR45|11152|Transcript|NM_007075.4|protein_coding||10/11|NM_007075.4:c.830+2T>A|||||||CS135341|1||-1||1|EntrezGene||||||||||1|||||||||27|28|-2|2|0.02|0.00|0.01|0.99|WDR45|VUS|0.9742088||||||HP:0000951||1.088||XL||LP||||8.134000||||||||LP|filter&vkgl&exit_lp,T|upstream_gene_variant|MODIFIER|PRAF2|11230|Transcript|NM_007213.3|protein_coding||||||||||CS135341|1|1360|-1|||EntrezGene||||||||||1|||||||||27|28|-2|2|0.02|0.00|0.01|0.99|WDR45|VUS|0.7629854||||||||-0.375||||||||8.134000||||||||LP|filter&vkgl&clinVar&gnomAD&sv&spliceAI&exit_lp,T|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001477865|CTCF_binding_site||||||||||CS135341|1|||||||||||||||1|||||||||||||||||||||||||||||||||||8.134000||||||||LQ|exit_rm,T|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001765299|promoter_flanking_region||||||||||CS135341|1|||||||||||||||1|||||||||||||||||||||||||||||||||||8.134000||||||||LQ|exit_rm;VIPC_S=OK GT:AD:DP:GQ:VID:VIM:VIPC_S:VIPP_S 1|0:25,25:50:50:1:0:OK,OK,OK,OK,OK:GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1,GQ&DP&VIM&VID&exit_u1 1|0:25,25:50:50:.:.:.:. 0|0:50,0:50:50:.:.:.:. 1|1:0,50:50:50:.:.:.:. 0|0:50,0:50:50:.:.:.:. 1|1:0,50:50:50:.:.:.:.
134
134
  Y 2655641 y_chrom G A . PASS CSQ=A|stop_gained|HIGH|SRY|6736|Transcript|NM_003140.3|protein_coding|1/1||NM_003140.3:c.4C>T|NP_003131.1:p.Gln2Ter|83/828|4/615|2/204|Q/*|Caa/Taa|rs104894977&CM981858|1||-1||1|EntrezGene||||||||pathogenic||1&1|2401216&9443877||||||||-26|-50|2|-4|0.01|0.00|0.00|0.00|SRY|VUS|0.85415643||||||||2.02||||||||0.170000||||9753|Pathogenic||no_assertion_criteria_provided|LP|filter&vkgl&clinVar&exit_lp;VIPC_S=OK GT:AD:DP:GQ:VID:VIM:VIPC_S:VIPP_S 1:50:50:50:1:0:OK:GQ&DP&VIM&VID&exit_u1 0:.:10:50:.:.:.:. .:.:.:50:.:.:.:. .:.:.:50:.:.:.:. 1:50:50:50:.:.:.:. 1:50:50:50:.:.:.:.
package/src/mocks/GRCh38/field_metadata.json CHANGED
@@ -203,9 +203,13 @@
203
203
  "label": "P",
204
204
  "description": "Pathogenic"
205
205
  },
206
- "Conflicting_interpretations_of_pathogenicity": {
206
+ "Conflicting_classifications_of_pathogenicity": {
207
207
  "label": "Conflict",
208
- "description": "Conflicting interpretations of pathogenicity"
208
+ "description": "Conflicting classifications of pathogenicity"
209
+ },
210
+ "Other": {
211
+ "label": "Other",
212
+ "description": "Classifications that do not match the common categorical values."
209
213
  }
210
214
  }
211
215
  },
@@ -236,9 +240,9 @@
236
240
  "label": "P",
237
241
  "description": "Pathogenic"
238
242
  },
239
- "Conflicting_interpretations_of_pathogenicity": {
243
+ "Conflicting_classifications_of_pathogenicity": {
240
244
  "label": "Conflict",
241
- "description": "Conflicting interpretations of pathogenicity"
245
+ "description": "Conflicting classifications of pathogenicity"
242
246
  }
243
247
  }
244
248
  },
@@ -273,8 +277,8 @@
273
277
  "label": "Single submitter",
274
278
  "description": "There is a single submitted record with a classification"
275
279
  },
276
- "_conflicting_interpretations": {
277
- "label": "Conflicting_interpretations",
280
+ "_conflicting_classifications": {
281
+ "label": "Conflicting_classifications",
278
282
  "description": "There are conflicting classifications"
279
283
  },
280
284
  "no_assertion_criteria_provided": {
@@ -283,6 +287,15 @@
283
287
  },
284
288
  "no_assertion_provided": {
285
289
  "label": "No assertion provided"
290
+ },
291
+ "no_classification_for_the_single_variant": {
292
+ "label": "No classification for the single variant"
293
+ },
294
+ "no_classification_provided": {
295
+ "label": "No classification provided"
296
+ },
297
+ "no_classifications_from_unflagged_records": {
298
+ "label": "No classifications from unflagged records"
286
299
  }
287
300
  }
288
301
  },
@@ -765,8 +778,8 @@
765
778
  "STR_STATUS": {
766
779
  "label": "STR status",
767
780
  "description": "Repeat expansion status as decided by Stranger",
768
- "numberType": "NUMBER",
769
- "numberCount": 1,
781
+ "numberType": "PER_ALT",
782
+ "separator": ",",
770
783
  "type": "CATEGORICAL",
771
784
  "categories": {
772
785
  "normal": {