@molgenis/vip-report-template 5.6.0 → 5.8.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (25) hide show
  1. package/.nvmrc +1 -0
  2. package/.travis.yml +0 -2
  3. package/package.json +22 -22
  4. package/src/components/filter/Filter.tsx +12 -0
  5. package/src/components/filter/FilterCategorical.tsx +26 -19
  6. package/src/components/filter/FilterGene.tsx +34 -0
  7. package/src/components/filter/FilterHpo.tsx +33 -27
  8. package/src/components/filter/FilterInheritance.tsx +39 -9
  9. package/src/components/filter/FilterIntegerDp.tsx +19 -4
  10. package/src/components/filter/FilterIntegerGq.tsx +19 -4
  11. package/src/components/filter/FilterVI.tsx +68 -0
  12. package/src/components/filter/FilterVariantType.tsx +148 -0
  13. package/src/components/filter/InfoFilter.tsx +1 -13
  14. package/src/components/filter/InfoFilters.tsx +4 -1
  15. package/src/components/filter/SampleFilters.tsx +26 -2
  16. package/src/components/record/info/GnomAD.tsx +33 -28
  17. package/src/mocks/GRCh37/vcf/family.vcf.blob +5 -4
  18. package/src/views/SampleVariants.tsx +52 -5
  19. package/src/views/data/SampleData.tsx +2 -0
  20. package/src/views/data/SampleVariantConsequenceData.tsx +1 -0
  21. package/src/views/data/SampleVariantData.tsx +1 -0
  22. package/src/views/data/VariantConsequenceData.tsx +1 -0
  23. package/src/views/data/VariantData.tsx +1 -0
  24. package/tsconfig.json +1 -1
  25. package/{vite.config.ts → vite.config.mts} +2 -2
package/.nvmrc ADDED
@@ -0,0 +1 @@
1
+ 18.18.2
package/.travis.yml CHANGED
@@ -1,8 +1,6 @@
1
1
  os: linux
2
2
  dist: focal
3
3
  language: node_js
4
- node_js:
5
- - 18
6
4
  branches:
7
5
  only:
8
6
  - main
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@molgenis/vip-report-template",
3
- "version": "5.6.0",
3
+ "version": "5.8.0",
4
4
  "description": "Report Template for Variant Call Format (VCF) Report Generator",
5
5
  "scripts": {
6
6
  "build": "vite build",
@@ -15,33 +15,33 @@
15
15
  },
16
16
  "license": "LGPL-3.0",
17
17
  "devDependencies": {
18
- "@molgenis/vite-plugin-inline": "^1.0.14",
19
- "@typescript-eslint/eslint-plugin": "^6.6.0",
20
- "@typescript-eslint/parser": "^6.6.0",
21
- "@vitest/coverage-v8": "^0.34.4",
18
+ "@molgenis/vite-plugin-inline": "^1.0.19",
19
+ "@typescript-eslint/eslint-plugin": "^6.13.2",
20
+ "@typescript-eslint/parser": "^6.13.2",
21
+ "@vitest/coverage-v8": "^1.0.1",
22
22
  "bulma": "^0.9.4",
23
- "eslint": "^8.49.0",
24
- "eslint-config-prettier": "^9.0.0",
25
- "eslint-plugin-prettier": "^5.0.0",
23
+ "eslint": "^8.55.0",
24
+ "eslint-config-prettier": "^9.1.0",
25
+ "eslint-plugin-prettier": "^5.0.1",
26
26
  "eslint-plugin-solid": "^0.13.0",
27
27
  "husky": "^8.0.3",
28
- "jsdom": "^22.1.0",
29
- "prettier": "^3.0.3",
30
- "sass": "^1.66.1",
31
- "typescript": "^5.2.2",
32
- "vite": "^4.4.9",
33
- "vite-plugin-solid": "^2.7.0",
34
- "vitest": "^0.34.4"
28
+ "jsdom": "^23.0.1",
29
+ "prettier": "^3.1.0",
30
+ "sass": "^1.69.5",
31
+ "typescript": "^5.3.3",
32
+ "vite": "^5.0.6",
33
+ "vite-plugin-solid": "^2.7.2",
34
+ "vitest": "^1.0.1"
35
35
  },
36
36
  "dependencies": {
37
- "@fortawesome/fontawesome-svg-core": "^6.4.2",
38
- "@fortawesome/free-solid-svg-icons": "^6.4.2",
39
- "@molgenis/vip-report-api": "^4.5.0",
40
- "@molgenis/vip-report-vcf": "^1.5.0",
41
- "@solidjs/router": "^0.8.3",
37
+ "@fortawesome/fontawesome-svg-core": "^6.5.1",
38
+ "@fortawesome/free-solid-svg-icons": "^6.5.1",
39
+ "@molgenis/vip-report-api": "^4.8.0",
40
+ "@molgenis/vip-report-vcf": "^1.8.0",
41
+ "@solidjs/router": "^0.9.1",
42
42
  "base64-js": "^1.5.1",
43
- "igv": "^2.15.10",
44
- "solid-js": "^1.7.11"
43
+ "igv": "^2.15.11",
44
+ "solid-js": "^1.8.7"
45
45
  },
46
46
  "lint-staged": {
47
47
  "src/**/*.{tsx,ts}": [
package/src/components/filter/Filter.tsx CHANGED
@@ -9,6 +9,9 @@ import { isAnyCsqInfo } from "../../utils/csqUtils";
9
9
  import { FilterChangeEvent, FilterClearEvent } from "./Filters";
10
10
  import { FilterAllelicBalance } from "./FilterAllelicBalance";
11
11
  import { FilterHpo } from "./FilterHpo";
12
+ import { FilterGene } from "./FilterGene";
13
+ import { FilterVI } from "./FilterVI";
14
+ import { FilterVariantType } from "./FilterVariantType";
12
15
 
13
16
  export type FilterProps = {
14
17
  field: FieldMetadata;
@@ -31,12 +34,21 @@ export const Filter: Component<FilterProps> = (props) => {
31
34
  <Match when={props.field.id === "VIAB"}>
32
35
  <FilterAllelicBalance {...props} />
33
36
  </Match>
37
+ <Match when={props.field.id === "VI"}>
38
+ <FilterVI {...props} />
39
+ </Match>
40
+ <Match when={props.field.id === "SVTYPE"}>
41
+ <FilterVariantType {...props} />
42
+ </Match>
34
43
  <Match when={isAnyCsqInfo(props.field, ["clinVar_CLNSIG", "clinVar_CLNSIGINCL"])}>
35
44
  <FilterClinVar {...props} />
36
45
  </Match>
37
46
  <Match when={props.field.id === "HPO"}>
38
47
  <FilterHpo {...props} />
39
48
  </Match>
49
+ <Match when={props.field.id === "IncompletePenetrance"}>
50
+ <FilterGene {...props} />
51
+ </Match>
40
52
  <Match when={props.field.type === "CATEGORICAL"}>
41
53
  <FilterCategorical {...props} />
42
54
  </Match>
package/src/components/filter/FilterCategorical.tsx CHANGED
@@ -17,6 +17,7 @@ export const FilterCategorical: Component<
17
17
  }
18
18
  > = (props) => {
19
19
  const group: CheckboxGroup = {};
20
+ const label = () => (props.field.label !== undefined ? props.field.label : props.field.id);
20
21
  if (props.query !== undefined) {
21
22
  (props.query?.args as string[]).forEach((key) => {
22
23
  group[key] = true;
@@ -49,26 +50,32 @@ export const FilterCategorical: Component<
49
50
 
50
51
  return (
51
52
  <>
52
- <For each={props.field.categories}>
53
- {(category) => (
54
- <div class="control">
55
- <Checkbox
56
- value={category}
57
- label={props.labels ? props.labels[category] : category}
58
- checked={props.query && (props.query.args as (string | null)[]).includes(category)}
59
- onChange={onChange}
60
- />
61
- </div>
53
+ <p class="has-text-weight-semibold">
54
+ {props.field.description ? <abbr title={props.field.description}>{label()}</abbr> : <span>{label()}</span>}
55
+ </p>
56
+
57
+ <div class="field">
58
+ <For each={props.field.categories}>
59
+ {(category) => (
60
+ <div class="control">
61
+ <Checkbox
62
+ value={category}
63
+ label={props.labels ? props.labels[category] : category}
64
+ checked={props.query && (props.query.args as (string | null)[]).includes(category)}
65
+ onChange={onChange}
66
+ />
67
+ </div>
68
+ )}
69
+ </For>
70
+ {includeNullCategory() && (
71
+ <Checkbox
72
+ value={nullValue}
73
+ label="No value"
74
+ checked={props.query && (props.query.args as (string | null)[]).includes(null)}
75
+ onChange={onChange}
76
+ />
62
77
  )}
63
- </For>
64
- {includeNullCategory() && (
65
- <Checkbox
66
- value={nullValue}
67
- label="No value"
68
- checked={props.query && (props.query.args as (string | null)[]).includes(null)}
69
- onChange={onChange}
70
- />
71
- )}
78
+ </div>
72
79
  </>
73
80
  );
74
81
  };
package/src/components/filter/FilterGene.tsx ADDED
@@ -0,0 +1,34 @@
1
+ import { Component } from "solid-js";
2
+ import { FilterProps } from "./Filter";
3
+ import { Checkbox, CheckboxEvent } from "../Checkbox";
4
+ import { selector, selectorKey } from "../../utils/query";
5
+
6
+ export const FilterGene: Component<FilterProps> = (props) => {
7
+ const onFilterChange = (event: CheckboxEvent) => {
8
+ const fieldSelector = selector(props.field);
9
+ if (event.checked) {
10
+ props.onChange({
11
+ key: selectorKey(fieldSelector),
12
+ query: {
13
+ selector: fieldSelector,
14
+ operator: "any_has_any",
15
+ args: ["1"],
16
+ },
17
+ });
18
+ } else props.onClear({ key: selectorKey(fieldSelector) });
19
+ };
20
+
21
+ return (
22
+ <>
23
+ <p class="has-text-weight-semibold">{<span>Various</span>}</p>
24
+ <div class="field">
25
+ <Checkbox
26
+ desc="Gene is associated with incomplete penetrance"
27
+ label="Inc. Penetrance"
28
+ checked={props.query && props.query.args !== undefined}
29
+ onChange={onFilterChange}
30
+ />
31
+ </div>
32
+ </>
33
+ );
34
+ };
package/src/components/filter/FilterHpo.tsx CHANGED
@@ -21,6 +21,7 @@ export const FilterHpo: Component<
21
21
  const group: CheckboxGroup = {};
22
22
  const hpoSelector = selector(props.field);
23
23
  const csqMeta = props.field.parent;
24
+ const label = () => (props.field.label !== undefined ? props.field.label : props.field.id);
24
25
  let gadoHcChecked = false;
25
26
  let gadoLcChecked = false;
26
27
  let hpoValues: (string | null)[] = [];
@@ -118,38 +119,43 @@ export const FilterHpo: Component<
118
119
  };
119
120
  return (
120
121
  <>
121
- <For each={props.field.categories}>
122
- {(category) => (
122
+ <p class="has-text-weight-semibold">
123
+ {props.field.description ? <abbr title={props.field.description}>{label()}</abbr> : <span>{label()}</span>}
124
+ </p>
125
+ <div class="field">
126
+ <For each={props.field.categories}>
127
+ {(category) => (
128
+ <div class="control">
129
+ <Checkbox
130
+ value={category}
131
+ label={props.labels ? props.labels[category] : category}
132
+ checked={hpoValues && hpoValues.includes(category)}
133
+ onChange={onChange}
134
+ />
135
+ </div>
136
+ )}
137
+ </For>
138
+ <Show when={gadoMeta !== null}>
123
139
  <div class="control">
124
140
  <Checkbox
125
- value={category}
126
- label={props.labels ? props.labels[category] : category}
127
- checked={hpoValues && hpoValues.includes(category)}
141
+ value="gado_hc"
142
+ label="GADO high"
143
+ desc="Gene predicted to have a relation with phenotypes of the proband (phenotypes of other samples are ignored!) with high confidence (Z-Score above 5)."
144
+ checked={gadoHcChecked}
128
145
  onChange={onChange}
129
146
  />
130
147
  </div>
131
- )}
132
- </For>
133
- <Show when={gadoMeta !== null}>
134
- <div class="control">
135
- <Checkbox
136
- value="gado_hc"
137
- label="GADO high"
138
- desc="Gene predicted to have a relation with phenotypes of the proband (phenotypes of other samples are ignored!) with high confidence (Z-Score above 5)."
139
- checked={gadoHcChecked}
140
- onChange={onChange}
141
- />
142
- </div>
143
- <div class="control">
144
- <Checkbox
145
- value="gado_lc"
146
- label="GADO low"
147
- desc="Gene predicted to have a relation with phenotypes of the proband (phenotypes of other samples are ignored!) with low confidence (Z-Score above 3 but below 5)."
148
- checked={gadoLcChecked}
149
- onChange={onChange}
150
- />
151
- </div>
152
- </Show>
148
+ <div class="control">
149
+ <Checkbox
150
+ value="gado_lc"
151
+ label="GADO low"
152
+ desc="Gene predicted to have a relation with phenotypes of the proband (phenotypes of other samples are ignored!) with low confidence (Z-Score above 3 but below 5)."
153
+ checked={gadoLcChecked}
154
+ onChange={onChange}
155
+ />
156
+ </div>
157
+ </Show>
158
+ </div>
153
159
  </>
154
160
  );
155
161
  };
package/src/components/filter/FilterInheritance.tsx CHANGED
@@ -17,11 +17,13 @@ export type FilterInheritanceProps = {
17
17
  export const FilterInheritance: Component<FilterInheritanceProps> = (props) => {
18
18
  const VIM_TRUE = "VIM_true";
19
19
  const VIM_MISSING = "VIM_missing";
20
- const VID = "VID";
20
+ const VID = "VID_true";
21
+ const VID_MISSING = "VID_missing";
21
22
 
22
23
  let isVimMissingChecked = false;
23
24
  let isVimTrueChecked = false;
24
- let isVidChecked = false;
25
+ let isVidTrueChecked = false;
26
+ let isVidMissingChecked = false;
25
27
 
26
28
  const vimFieldSelector: Selector = ["s", props.sample.data.index, ...selector(props.vimField)];
27
29
  const vidFieldSelector: Selector = ["s", props.sample.data.index, ...selector(props.vidField)];
@@ -37,7 +39,12 @@ export const FilterInheritance: Component<FilterInheritanceProps> = (props) => {
37
39
  ) {
38
40
  isVimMissingChecked = true;
39
41
  } else if (selectorKeyValue === selectorKey(vidFieldSelector) && query.args === 1) {
40
- isVidChecked = true;
42
+ isVidTrueChecked = true;
43
+ } else if (
44
+ selectorKeyValue === selectorKey(vidFieldSelector) &&
45
+ (query.args === null || query.args === undefined)
46
+ ) {
47
+ isVidMissingChecked = true;
41
48
  }
42
49
  });
43
50
  }
@@ -71,15 +78,29 @@ export const FilterInheritance: Component<FilterInheritanceProps> = (props) => {
71
78
  } else if (isVimMissingChecked && event.value === VIM_MISSING && !event.checked) {
72
79
  isVimMissingChecked = false;
73
80
  }
74
- if ((event.value === VID && event.checked) || (isVidChecked && event.value !== VID)) {
81
+ if ((event.value === VID && event.checked) || (isVidTrueChecked && event.value !== VID)) {
75
82
  queries.push({
76
83
  selector: vidFieldSelector,
77
84
  operator: "==",
78
85
  args: 1,
79
86
  });
80
- isVidChecked = true;
81
- } else if (isVidChecked && event.value === VID && !event.checked) {
82
- isVidChecked = false;
87
+ isVidTrueChecked = true;
88
+ } else if ((event.value === VID_MISSING && event.checked) || (isVidMissingChecked && event.value !== VID_MISSING)) {
89
+ queries.push(
90
+ {
91
+ selector: vidFieldSelector,
92
+ operator: "==",
93
+ args: null,
94
+ },
95
+ {
96
+ selector: vidFieldSelector,
97
+ operator: "==",
98
+ args: undefined,
99
+ },
100
+ );
101
+ isVimMissingChecked = true;
102
+ } else if (isVidTrueChecked && event.value === VID && !event.checked) {
103
+ isVidTrueChecked = false;
83
104
  }
84
105
  if (queries.length > 0) {
85
106
  props.onChange({
@@ -108,7 +129,7 @@ export const FilterInheritance: Component<FilterInheritanceProps> = (props) => {
108
129
  <div class="control">
109
130
  <Checkbox
110
131
  value={VIM_MISSING}
111
- label="Match: Possible"
132
+ label="Match: Potential"
112
133
  desc="Genotypes, affected statuses match but gene inheritance pattern is unknown (can include de novo variants)."
113
134
  checked={isVimMissingChecked}
114
135
  onChange={onFilterChange}
@@ -123,7 +144,16 @@ export const FilterInheritance: Component<FilterInheritanceProps> = (props) => {
123
144
  On the X chromosome:
124
145
  - Female proband: same as autosomes.
125
146
  - Male proband: Mother does not have the variant, or mother genotype missing."
126
- checked={isVidChecked}
147
+ checked={isVidTrueChecked}
148
+ onChange={onFilterChange}
149
+ />
150
+ </div>
151
+ <div class="control">
152
+ <Checkbox
153
+ value={VID_MISSING}
154
+ label="De novo: Potential"
155
+ desc="Variant could be denovo but some genotype data of the sample or parents is missing."
156
+ checked={isVidTrueChecked}
127
157
  onChange={onFilterChange}
128
158
  />
129
159
  </div>
package/src/components/filter/FilterIntegerDp.tsx CHANGED
@@ -11,9 +11,24 @@ export const FilterIntegerDp: Component<FilterProps> = (props) => {
11
11
  props.onChange({
12
12
  key: selectorKey(fieldSelector),
13
13
  query: {
14
- selector: fieldSelector,
15
- operator: ">=",
16
- args: 20,
14
+ operator: "or",
15
+ args: [
16
+ {
17
+ selector: fieldSelector,
18
+ operator: ">=",
19
+ args: 20,
20
+ },
21
+ {
22
+ selector: fieldSelector,
23
+ operator: "==",
24
+ args: null,
25
+ },
26
+ {
27
+ selector: fieldSelector,
28
+ operator: "==",
29
+ args: undefined,
30
+ },
31
+ ],
17
32
  },
18
33
  });
19
34
  else props.onClear({ key: selectorKey(fieldSelector) });
@@ -24,7 +39,7 @@ export const FilterIntegerDp: Component<FilterProps> = (props) => {
24
39
  <Checkbox
25
40
  desc="Sequencing depth >= 20"
26
41
  label="Depth >= 20"
27
- checked={props.query && props.query.args === 20}
42
+ checked={props.query && props.query.args !== undefined}
28
43
  onChange={onFilterChange}
29
44
  />
30
45
  </div>
package/src/components/filter/FilterIntegerGq.tsx CHANGED
@@ -11,9 +11,24 @@ export const FilterIntegerGq: Component<FilterProps> = (props) => {
11
11
  props.onChange({
12
12
  key: selectorKey(fieldSelector),
13
13
  query: {
14
- selector: fieldSelector,
15
- operator: ">=",
16
- args: 20,
14
+ operator: "or",
15
+ args: [
16
+ {
17
+ selector: fieldSelector,
18
+ operator: ">=",
19
+ args: 20,
20
+ },
21
+ {
22
+ selector: fieldSelector,
23
+ operator: "==",
24
+ args: null,
25
+ },
26
+ {
27
+ selector: fieldSelector,
28
+ operator: "==",
29
+ args: undefined,
30
+ },
31
+ ],
17
32
  },
18
33
  });
19
34
  else props.onClear({ key: selectorKey(fieldSelector) });
@@ -24,7 +39,7 @@ export const FilterIntegerGq: Component<FilterProps> = (props) => {
24
39
  <Checkbox
25
40
  desc="Genotype quality >= 20"
26
41
  label="GT quality >= 20"
27
- checked={props.query && props.query.args === 20}
42
+ checked={props.query && props.query.args !== undefined}
28
43
  onChange={onFilterChange}
29
44
  />
30
45
  </div>
package/src/components/filter/FilterVI.tsx ADDED
@@ -0,0 +1,68 @@
1
+ import { Component, For } from "solid-js";
2
+ import { Checkbox, CheckboxEvent } from "../Checkbox";
3
+ import { FilterProps } from "./Filter";
4
+ import { selector, selectorKey } from "../../utils/query";
5
+ import { Item, Sample, Selector } from "@molgenis/vip-report-api/src/Api";
6
+
7
+ export type CheckboxGroup = {
8
+ [key: string]: boolean;
9
+ };
10
+
11
+ export type CategoryDescriptions = {
12
+ [key: string]: string;
13
+ };
14
+
15
+ const labels: CategoryDescriptions = {
16
+ AR_C: "Autosomal Recessive: Compound Hetrozygote",
17
+ AD_IP: "Autosomal Dominant: Incomplete Penentrance",
18
+ AR: "Autosomal Recessive",
19
+ AD: "Autosomal Dominant",
20
+ XLD: "X-Linked Dominant",
21
+ XLR: "X-Linked Recessive",
22
+ };
23
+
24
+ export const FilterVI: Component<FilterProps> = (props) => {
25
+ const group: CheckboxGroup = {};
26
+ if (props.query !== undefined) {
27
+ (props.query?.args as string[]).forEach((key) => {
28
+ group[key] = true;
29
+ });
30
+ }
31
+
32
+ // enable null category for any_has_any case if someone asks for it (requires query to be composed)
33
+ const fieldSelector: Selector = ["s", (props.sample as Item<Sample>).data.index, ...selector(props.field)];
34
+ const onChange = (event: CheckboxEvent) => {
35
+ group[event.value] = event.checked;
36
+ const values = Object.keys(group).filter((key) => group[key]);
37
+ if (values.length > 0) {
38
+ props.onChange({
39
+ key: selectorKey(fieldSelector),
40
+ query: {
41
+ selector: fieldSelector,
42
+ operator: "has_any",
43
+ args: values,
44
+ },
45
+ });
46
+ } else {
47
+ props.onClear({ key: selectorKey(fieldSelector) });
48
+ }
49
+ };
50
+
51
+ return (
52
+ <>
53
+ <For each={props.field.categories}>
54
+ {(category) => (
55
+ <div class="control">
56
+ <Checkbox
57
+ value={category}
58
+ label={category}
59
+ desc={labels[category] !== undefined ? labels[category] : category}
60
+ checked={props.query && (props.query.args as (string | null)[]).includes(category)}
61
+ onChange={onChange}
62
+ />
63
+ </div>
64
+ )}
65
+ </For>
66
+ </>
67
+ );
68
+ };
package/src/components/filter/FilterVariantType.tsx ADDED
@@ -0,0 +1,148 @@
1
+ import { Component } from "solid-js";
2
+ import { Checkbox, CheckboxEvent } from "../Checkbox";
3
+ import { FilterProps } from "./Filter";
4
+ import { selector, selectorKey } from "../../utils/query";
5
+ import { ComposedQuery, Query, QueryClause } from "@molgenis/vip-report-api/src/Api";
6
+
7
+ export type CheckboxGroup = {
8
+ [key: string]: boolean;
9
+ };
10
+
11
+ export type CategoryLabels = {
12
+ [key: string]: string;
13
+ };
14
+
15
+ export const FilterVariantType: Component<
16
+ FilterProps & {
17
+ labels?: CategoryLabels;
18
+ }
19
+ > = (props) => {
20
+ const group: CheckboxGroup = {};
21
+ let snvChecked = false;
22
+ let strChecked = false;
23
+ let svChecked = false;
24
+ const svSelector = selector(props.field);
25
+ const strQuery: QueryClause = {
26
+ selector: svSelector,
27
+ operator: "==",
28
+ args: "STR",
29
+ };
30
+
31
+ const svQuery: ComposedQuery = {
32
+ operator: "and",
33
+ args: [
34
+ {
35
+ selector: svSelector,
36
+ operator: "!=",
37
+ args: "STR",
38
+ },
39
+ {
40
+ selector: svSelector,
41
+ operator: "!=",
42
+ args: null,
43
+ },
44
+ {
45
+ selector: svSelector,
46
+ operator: "!=",
47
+ args: undefined,
48
+ },
49
+ ],
50
+ };
51
+
52
+ const snvQuery: ComposedQuery = {
53
+ operator: "or",
54
+ args: [
55
+ {
56
+ selector: svSelector,
57
+ operator: "==",
58
+ args: null,
59
+ },
60
+ {
61
+ selector: svSelector,
62
+ operator: "==",
63
+ args: undefined,
64
+ },
65
+ ],
66
+ };
67
+
68
+ if (props.query !== undefined && props.query.args.length > 0) {
69
+ console.log(props.query);
70
+ const query: Query = props.query.args[0] as Query;
71
+ (query.args as Query[]).forEach((childQuery) => {
72
+ if (childQuery.operator == "and") {
73
+ group["SNV"] = true;
74
+ snvChecked = true;
75
+ }
76
+ if (childQuery.operator == "or") {
77
+ group["SV"] = true;
78
+ svChecked = true;
79
+ }
80
+ if (childQuery.operator == "==") {
81
+ group["STR"] = true;
82
+ strChecked = true;
83
+ }
84
+ });
85
+ }
86
+ const onChange = (event: CheckboxEvent) => {
87
+ const queries: Query[] = [];
88
+ group[event.value] = event.checked;
89
+ const values = Object.keys(group).filter((key) => group[key]);
90
+ if (values.length > 0) {
91
+ if (values.includes("SNV")) {
92
+ queries.push(snvQuery);
93
+ snvChecked = true;
94
+ } else {
95
+ snvChecked = false;
96
+ }
97
+ if (values.includes("STR")) {
98
+ queries.push(strQuery);
99
+ strChecked = true;
100
+ } else {
101
+ strChecked = false;
102
+ }
103
+ if (values.includes("SV")) {
104
+ queries.push(svQuery);
105
+ svChecked = true;
106
+ } else {
107
+ svChecked = false;
108
+ }
109
+ props.onChange({
110
+ key: selectorKey(svSelector),
111
+ query: {
112
+ operator: "or",
113
+ args: queries,
114
+ },
115
+ });
116
+ } else {
117
+ props.onClear({ key: selectorKey(svSelector) });
118
+ }
119
+ };
120
+
121
+ return (
122
+ <>
123
+ <p class="has-text-weight-semibold">
124
+ <abbr title={"Only show variants of a certain type (called by a specific variant caller)."}>
125
+ {"Variant type"}
126
+ </abbr>
127
+ </p>
128
+
129
+ <div class="field">
130
+ <div class="control">
131
+ <Checkbox
132
+ value="SNV"
133
+ label="SNV/Indel"
134
+ desc="Single nucleotide variants and short InDels."
135
+ checked={snvChecked}
136
+ onChange={onChange}
137
+ />
138
+ </div>
139
+ <div class="control">
140
+ <Checkbox value="SV" label="SV" desc="Structural variants." checked={svChecked} onChange={onChange} />
141
+ </div>
142
+ <div class="control">
143
+ <Checkbox value="STR" label="STR" desc="Short Tandem Repeats." checked={strChecked} onChange={onChange} />
144
+ </div>
145
+ </div>
146
+ </>
147
+ );
148
+ };
package/src/components/filter/InfoFilter.tsx CHANGED
@@ -5,8 +5,6 @@ import { ComposedQuery, Query, QueryClause, SelectorPart } from "@molgenis/vip-r
5
5
  import { selectorKey } from "../../utils/query";
6
6
 
7
7
  export const InfoFilter: Component<FilterProps> = (props) => {
8
- const label = () => (props.field.label !== undefined ? props.field.label : props.field.id);
9
-
10
8
  const onChange = (event: FilterChangeEvent) => {
11
9
  props.onChange({
12
10
  key: selectorKey(["n", event.key]),
@@ -37,15 +35,5 @@ export const InfoFilter: Component<FilterProps> = (props) => {
37
35
  key: selectorKey(["n", event.key]),
38
36
  });
39
37
  };
40
-
41
- return (
42
- <>
43
- <p class="has-text-weight-semibold">
44
- {props.field.description ? <abbr title={props.field.description}>{label()}</abbr> : <span>{label()}</span>}
45
- </p>
46
- <div class="field">
47
- <Filter field={props.field} query={props.query} onChange={onChange} onClear={onClear} />
48
- </div>
49
- </>
50
- );
38
+ return <Filter field={props.field} query={props.query} onChange={onChange} onClear={onClear} />;
51
39
  };
package/src/components/filter/InfoFilters.tsx CHANGED
@@ -13,7 +13,10 @@ export const InfoFilters: Component<{
13
13
  onClear: (event: FilterClearEvent) => void;
14
14
  defaultValues?: { [key: string]: Value };
15
15
  }> = (props) => {
16
- const filterableFields = () => props.fields.filter((field) => field.type === "CATEGORICAL");
16
+ const filterableFields = () =>
17
+ props.fields.filter(
18
+ (field) => field.type === "CATEGORICAL" || field.id === "IncompletePenetrance" || field.id === "SVTYPE",
19
+ );
17
20
 
18
21
  return (
19
22
  <>
package/src/components/filter/SampleFilters.tsx CHANGED
@@ -6,6 +6,7 @@ import { FilterQueries } from "../../store";
6
6
  import { sampleCustomKey, sampleFieldKey } from "../../utils/query";
7
7
  import { FilterChangeEvent, FilterClearEvent } from "./Filters";
8
8
  import { FilterInheritance } from "./FilterInheritance";
9
+ import { FilterVI } from "./FilterVI";
9
10
 
10
11
  export const SampleFilters: Component<{
11
12
  sample: Item<Sample>;
@@ -18,14 +19,17 @@ export const SampleFilters: Component<{
18
19
  throw Error("Cannot create Sample filters without a sample.");
19
20
  }
20
21
 
21
- const qualityFields = props.fields.filter((field) => field.id !== "VIM" && field.id !== "VID");
22
+ const qualityFields = props.fields.filter((field) => field.id !== "VIM" && field.id !== "VID" && field.id !== "VI");
22
23
  let vimField: FieldMetadata | undefined;
23
24
  let vidField: FieldMetadata | undefined;
25
+ let viField: FieldMetadata | undefined;
24
26
  props.fields.forEach((field) => {
25
27
  if (field.id === "VIM") {
26
28
  vimField = field;
27
29
  } else if (field.id === "VID") {
28
30
  vidField = field;
31
+ } else if (field.id === "VI") {
32
+ viField = field;
29
33
  }
30
34
  });
31
35
 
@@ -33,7 +37,9 @@ export const SampleFilters: Component<{
33
37
  return (
34
38
  <>
35
39
  <Show when={vimField !== undefined && vidField !== undefined}>
36
- <p class="has-text-weight-semibold">{props.sample.data.person.individualId}: Inheritance</p>
40
+ <abbr class="has-text-weight-semibold" title="Inheritance Match">
41
+ {props.sample.data.person.individualId} Inh. Match
42
+ </abbr>
37
43
  <div class="field">
38
44
  {" "}
39
45
  <FilterInheritance
@@ -47,6 +53,24 @@ export const SampleFilters: Component<{
47
53
  />
48
54
  </div>
49
55
  </Show>
56
+ <Show when={viField !== undefined}>
57
+ <abbr
58
+ class="has-text-weight-semibold"
59
+ title="Inheritance Modes that are suitable for the pedigree genotypes and affected statuses"
60
+ >
61
+ {props.sample.data.person.individualId} Inh. Modes
62
+ </abbr>
63
+ <div class="field">
64
+ {" "}
65
+ <FilterVI
66
+ field={viField as FieldMetadata}
67
+ query={props.queries ? props.queries[sampleFieldKey(props.sample, viField as FieldMetadata)] : undefined}
68
+ onChange={props.onChange}
69
+ onClear={props.onClear}
70
+ sample={props.sample}
71
+ />
72
+ </div>
73
+ </Show>
50
74
  <p class="has-text-weight-semibold">{props.sample.data.person.individualId}: Quality</p>
51
75
  <div class="field">
52
76
  <For each={qualityFields}>
package/src/components/record/info/GnomAD.tsx CHANGED
@@ -3,47 +3,52 @@ import { FieldValueFloat } from "../field/FieldValueFloat";
3
3
  import { FieldProps } from "../field/Field";
4
4
  import { ValueFloat } from "@molgenis/vip-report-vcf/src/ValueParser";
5
5
  import { Anchor } from "../../Anchor";
6
+ import { getCsqInfo, getCsqInfoIndex } from "../../../utils/csqUtils";
6
7
 
7
8
  export const GnomAD: Component<FieldProps> = (props) => {
8
9
  const af = (): number | null => props.info.value as ValueFloat;
9
10
 
11
+ const qcIndex = (): number => getCsqInfoIndex(props.infoMeta, "gnomAD_QC");
12
+ const qc = (): string[] => (qcIndex() !== -1 ? (getCsqInfo(props.info, qcIndex()) as string[]) : []);
13
+ const covIndex = (): number => getCsqInfoIndex(props.infoMeta, "gnomAD_COV");
14
+ const cov = (): number | null => (covIndex() !== -1 ? (getCsqInfo(props.info, covIndex()) as number) : null);
15
+
10
16
  const href = (): string | undefined => {
11
17
  let href;
12
- if (af()) {
13
- let dataset;
14
- switch (props.context.genomeAssembly) {
15
- case "GRCh37":
16
- dataset = "gnomad_r2_1";
17
- break;
18
- case "GRCh38":
19
- dataset = "gnomad_r3";
20
- break;
21
- default:
22
- dataset = null;
23
- break;
24
- }
25
-
26
- if (dataset) {
27
- const record = props.info.record.data;
28
- // FIXME record.a incorrect: select record.a through CSQ:ALLELE_NUM
29
- const variantId = [record.c, record.p, record.r, record.a].join("-");
30
- href = `https://gnomad.broadinstitute.org/variant/${encodeURIComponent(variantId)}?dataset=${dataset}`;
31
- }
18
+ if (af() !== null) {
19
+ const record = props.info.record.data;
20
+ // FIXME record.a incorrect: select record.a through CSQ:ALLELE_NUM
21
+ const variantId = [record.c, record.p, record.r, record.a].join("-");
22
+ const dataset = "gnomad_r4";
23
+ href = `https://gnomad.broadinstitute.org/variant/${encodeURIComponent(variantId)}?dataset=${dataset}`;
32
24
  }
33
25
  return href;
34
26
  };
35
27
 
36
28
  return (
37
- <Show when={af()} keyed>
38
- {(af) => (
39
- <Show when={href()} fallback={<FieldValueFloat value={af} />} keyed>
40
- {(href) => (
29
+ <Show when={af() !== null}>
30
+ <Show when={href()} fallback={<FieldValueFloat value={af()} />} keyed>
31
+ {(href) => (
32
+ <>
41
33
  <Anchor href={href}>
42
- <FieldValueFloat value={af} />
34
+ <FieldValueFloat value={af()} />
43
35
  </Anchor>
44
- )}
45
- </Show>
46
- )}
36
+ <Show when={qc().length > 0}>
37
+ <abbr title={"Failed quality control filters: " + qc().join(", ")} class="ml-1 is-clickable">
38
+ <i class="fas fa-circle-exclamation has-text-warning" />
39
+ </abbr>
40
+ </Show>
41
+ <Show when={cov() != null && cov() < 0.5}>
42
+ <abbr
43
+ title="This variant is covered in fewer than 50% of individuals in gnomAD. This may indicate a low-quality site."
44
+ class="ml-1 is-clickable"
45
+ >
46
+ <i class="fas fa-circle-exclamation has-text-warning" />
47
+ </abbr>
48
+ </Show>
49
+ </>
50
+ )}
51
+ </Show>
47
52
  </Show>
48
53
  );
49
54
  };
package/src/mocks/GRCh37/vcf/family.vcf.blob CHANGED
@@ -98,9 +98,9 @@
98
98
  1 1701 . T C . PASS CSQ=C|intergenic_variant|MODIFIER||||||||||||||||1||||1||||||||||||||||||||||||||||||||||||||||||||||||||||||LQ|chrom&gene&exit_rm;DP=131;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIG:VIM:VIPC_S:VIPP_S 1|1:0,50:50:50:AR:1:64802:.:OK:HR&GQ&DP&VIM&VID&exit_ok 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.
99
99
  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|chrom&gene&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|chrom&gene&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|chrom&gene&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:LQ,LQ,LQ:HR&GQ&exit_lq,HR&GQ&exit_lq,HR&GQ&exit_lq 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:.:.:.:.:.:.
100
100
  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|chrom&gene&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|chrom&gene&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|chrom&gene&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|chrom&gene&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|chrom&gene&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|chrom&gene&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|chrom&gene&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|chrom&gene&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:HR&GQ&DP&VIM&exit_ok,HR&GQ&DP&VIM&exit_ok,HR&GQ&DP&VIM&exit_ok,HR&GQ&DP&VIM&exit_ok,HR&GQ&DP&VIM&exit_ok,HR&GQ&DP&VIM&exit_ok,HR&GQ&DP&VIM&exit_ok,HR&GQ&DP&VIM&exit_ok: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:.:.:.:.:.:.:.:.
101
- 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|chrom&gene&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|chrom&gene&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,AD:1_16376412_G_A,1_16375583_GA_G:1:1188:1:OK,OK:HR&GQ&DP&VIM&exit_ok,HR&GQ&DP&VIM&exit_ok:AR_C 0|0:50,0:50:50:.:.:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.:.:.
101
+ 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|chrom&gene&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|chrom&gene&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:HR&GQ&DP&VIM&exit_ok,HR&GQ&DP&VIM&exit_ok:AR_C 0|0:50,0:50:50:.:.:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.:.:.
102
102
  1 16376412 . G A . PASS CSQ=A|splice_donor_variant|HIGH|CLCNKB|1188|Transcript|NM_000085.5|protein_coding||10/19|NM_000085.5:c.968+1G>A|||||||rs201204502&CS1211892&CS971662|1||1||1|EntrezGene||||||||||0&1&1|||||||||17|-36|-28|-1|0.00|0.00|0.03|0.97|CLCNKB|VUS|0.9882061||||||HP:0000951||1.439||AR||LP||||4.909000|1:16376412-16376412|6.38086e-05|0|1285112|Pathogenic/Likely_pathogenic||no_assertion_criteria_provided|LP|chrom&gene&filter&vkgl&exit_lp,A|splice_donor_variant|HIGH|CLCNKB|1188|Transcript|NM_001165945.2|protein_coding||3/12|NM_001165945.2:c.461+1G>A|||||||rs201204502&CS1211892&CS971662|1||1|||EntrezGene||||||||||0&1&1|||||||||17|-36|-28|-1|0.00|0.00|0.03|0.97|CLCNKB|VUS|0.9882061||||||HP:0000951||1.439||AR||LP||||4.909000|1:16376412-16376412|6.38086e-05|0|1285112|Pathogenic/Likely_pathogenic||no_assertion_criteria_provided|LP|chrom&gene&filter&vkgl&exit_lp;VIPC_S=OK GT:AD:DP:GQ:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S:VIS 0|1:50:50:50:AR:1_16375583_GA_G,1_16376412_G_N:0:1188:1:OK,OK:HR&GQ&DP&VIM&exit_ok,HR&GQ&DP&VIM&exit_ok:AR_C 0|0:50,0:50:50:.:.:.:.:.:.:.:. 1|0:25,25:50:50:.:.:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.:.:.
103
- 1 17349219 g_ref G A . PASS CSQ=A|missense_variant|MODERATE|SDHB|6390|Transcript|NM_003000.3|protein_coding|7/8||NM_003000.3:c.649C>T|NP_002991.2:p.Arg217Cys|662/1015|649/843|217/280|R/C|Cgc/Tgc|rs200245469&CM094752&CM1210440&COSV64965760|1||-1||1|EntrezGene|||||0|1||likely_pathogenic|0&0&0&1|1&1&1&1||||||||180|28|6|6|5|0.00|0.00|0.00|0.00|SDHB|VUS|0.9769107||||||HP:0000951||2.452||AD&AR||LP||||9.093000||||183735|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|chrom&gene&filter&vkgl&exit_lp;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIG:VIM:VIPC_S:VIPP_S 1|1:0,50:50:50:AR:1:6390:1:OK:HR&GQ&DP&VIM&exit_ok 1|0:45,5:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 1|0:25,25:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.
103
+ 1 17349219 g_ref G A . PASS CSQ=A|missense_variant|MODERATE|SDHB|6390|Transcript|NM_003000.3|protein_coding|7/8||NM_003000.3:c.649C>T|NP_002991.2:p.Arg217Cys|662/1015|649/843|217/280|R/C|Cgc/Tgc|rs200245469&CM094752&CM1210440&COSV64965760|1||-1||1|EntrezGene|||||0|1||likely_pathogenic|0&0&0&1|1&1&1&1||||||||180|28|6|6|5|0.00|0.00|0.00|0.00|SDHB|VUS|0.9769107||||||HP:0000951||2.452||AD&AR||LP||||9.093000||||183735|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|chrom&gene&filter&vkgl&exit_lp;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIG:VIM:VIPC_S:VIPP_S 1|1:0,50:19:19:AR:1:6390:1:OK:HR&GQ&DP&VIM&exit_ok 1|0:45,5:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 1|0:25,25:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.
104
104
  1 17355094 . C T . PASS CSQ=T|splice_donor_variant|HIGH|SDHB|6390|Transcript|NM_003000.3|protein_coding||4/7|NM_003000.3:c.423+1G>A|||||||rs398122805&CS056774&CS062098&COSV64965540|1||-1||1|EntrezGene||||||||pathogenic|0&0&0&1|1&1&1&1|21348866&17667967&17804857&16405730&21565294&15383933||||||||-49|12|26|1|0.00|0.00|0.14|0.97|SDHB|VUS|0.991252||||||HP:0000951||2.452||AD&AR||LP||||7.131000|1:17355094-17355094|1.19344e-05|0|29896|Pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|chrom&gene&filter&vkgl&exit_lp;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIG:VIM:VIPC_S:VIPP_S 1|0:5,45:50:50:AD:1:6390:1:OK:HR&GQ&DP&VIM&exit_ok 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.
105
105
  1 152520788 symbolic1 A <DEL> . PASS CSQ=deletion|transcript_ablation|HIGH|LCE3D|84648|Transcript|NM_032563.2|protein_coding|||||||||||1||-1||1|EntrezGene|||||||||||||||||||||||||||||||||||||||||||||||||||||VUS|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&annotSV&spliceAI&utr5&capice&exit_vus,deletion|upstream_gene_variant|MODIFIER|LCE3C|353144|Transcript|NM_178434.3|protein_coding|||||||||||1|2608|1|||EntrezGene|||||||||||||||||||||||||||||||||||||||||||||||||||||VUS|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&annotSV&spliceAI&utr5&capice&exit_vus,deletion|transcript_ablation|HIGH|LCE3E|353145|Transcript|NM_178435.4|protein_coding|||||||||||1||-1|||EntrezGene|||||||||||||||||||||||||||||||||||||||||||||||||||||VUS|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&annotSV&spliceAI&utr5&capice&exit_vus,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000946440||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001787329||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000013752||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000946442||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000946443||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001505919||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001787330||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001787331||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001787332||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00701519957||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00905971885||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00522719201||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm;SVLEN=-49314;SVTYPE=DEL;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIM:VIPC_S:VIPP_S:VIC 1|1:0,50:50:50:AR:1:0:OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK:HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok:123456_A_C 0|0:50,0:50:50:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:. 1|0:25,25:50:50:.:.:.:.:.
106
106
  2 321682 . T <DEL> . PASS CSQ=deletion|non_coding_transcript_exon_variant&intron_variant&feature_truncation|MODIFIER|LINC01865|105373350|Transcript|NR_146953.1|lncRNA|3/4|3/3|||685-?/2100||||||1||1||1|EntrezGene||||||||||||||||||||||||||||||||||||||||||3|1A_(cf_Gene_count%2C_RE_gene%2C_+0.00)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(1_gene%2C_+0.00)%3B5F_(+0.00)|0.0|||||||||VUS|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&annotSV&exit_vus;END=321887;SVLEN=-205;SVTYPE=DEL;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIG:VIM:VIPC_S:VIPP_S 1|1:0,50:50:50:AR:0:64802:.:OK:HR&GQ&DP&VIM&VID&exit_ok 1|0:50,0:50:50:.:.:.:.:.:. 1|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.
@@ -117,11 +117,12 @@
117
117
  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|chrom&gene&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|chrom&gene&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|chrom&gene&filter&vkgl&exit_lp,G|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001573054|open_chromatin_region|||||||||||1||||||||||||||||||||||||||||||||||||||||||||||||||7.817000||||||||LQ|chrom&gene&exit_rm;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIM:VIPC_S:VIPP_S 1|1:0,50:50:50:AR:1:0:OK,OK,OK,OK:HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok 0|0:50,0:50:50:.:.:.:.:. 1|0:45,5:50:50:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:. 1|0:25,25:50:50:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.
118
118
  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|chrom&gene&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|chrom&gene&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:HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok 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:.:.:.:.
119
119
  17 29585422 . A G . PASS CSQ=G|missense_variant|MODERATE|NF1|4763|Transcript|NM_000267.3|protein_coding|31/57||NM_000267.3:c.4171A>G|NP_000258.1:p.Arg1391Gly|4554/12362|4171/8457|1391/2818|R/G|Aga/Gga|rs1555618515&CM1211610|1||1|||EntrezGene|||||0|0.962||pathogenic||1&1||||||||125|-48|2|28|-27|0.00|0.00|0.01|0.00|NF1|VUS|0.9277154||||||HP:0000951||0.583|1|AD||LP||||4.149000||||457686|Pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|chrom&gene&filter&vkgl&exit_lp,G|missense_variant|MODERATE|NF1|4763|Transcript|NM_001042492.3|protein_coding|32/58||NM_001042492.3:c.4234A>G|NP_001035957.1:p.Arg1412Gly|4567/12373|4234/8520|1412/2839|R/G|Aga/Gga|rs1555618515&CM1211610|1||1||1|EntrezGene|||||0|0.988||pathogenic||1&1||||||||125|-48|2|28|-27|0.00|0.00|0.01|0.00|NF1|VUS|0.97049046||||||HP:0000951||0.583|1|AD||LP||||4.149000||||457686|Pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|chrom&gene&filter&vkgl&exit_lp;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIM:VIPC_S:VIPP_S 1|1:0,50:50:.:AR:1:0:OK,OK:HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok 0|1:.:10:50:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.
120
- 17 29663879 . T G . PASS CSQ=G|missense_variant|MODERATE|NF1|4763|Transcript|NM_000267.3|protein_coding|41/57||NM_000267.3:c.6311T>G|NP_000258.1:p.Leu2104Arg|6694/12362|6311/8457|2104/2818|L/R|cTg/cGg|CM141499&CM143458|1||1|||EntrezGene|||||0|0.994||||1&1||||||||102|-42|41|-34|8|0.00|0.00|0.00|0.00|NF1|VUS|0.99390525||||||HP:0000951||0.583|1|AD||LP||||7.536000||||996527|Likely_pathogenic||criteria_provided&_single_submitter|LP|chrom&gene&filter&vkgl&exit_lp,G|missense_variant|MODERATE|NF1|4763|Transcript|NM_001042492.3|protein_coding|42/58||NM_001042492.3:c.6374T>G|NP_001035957.1:p.Leu2125Arg|6707/12373|6374/8520|2125/2839|L/R|cTg/cGg|CM141499&CM143458|1||1||1|EntrezGene|||||0|0.993||||1&1||||||||102|-42|41|-34|8|0.00|0.00|0.00|0.00|NF1|VUS|0.9962404||||||HP:0000951||0.583|1|AD||LP||||7.536000||||996527|Likely_pathogenic||criteria_provided&_single_submitter|LP|chrom&gene&filter&vkgl&exit_lp;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIG:VIM:VIPC_S:VIPP_S:VIS 1|0:25,25:50:50:AD:0:4763:1:OK,OK:HR&GQ&DP&VIM&exit_ok,HR&GQ&DP&VIM&exit_ok:AD_IP 0|0:50,0:50:50:.:.:.:.:.:.:. 1|0:25,25:50:50:.:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.:.
120
+ 17 29663879 . T G . PASS CSQ=G|missense_variant|MODERATE|NF1|4763|Transcript|NM_000267.3|protein_coding|41/57||NM_000267.3:c.6311T>G|NP_000258.1:p.Leu2104Arg|6694/12362|6311/8457|2104/2818|L/R|cTg/cGg|CM141499&CM143458|1||1|||EntrezGene|||||0|0.994||||1&1||||||||102|-42|41|-34|8|0.00|0.00|0.00|0.00|NF1|VUS|0.99390525||||||HP:0000951||0.583|1|AD||LP||||7.536000||||996527|Likely_pathogenic||criteria_provided&_single_submitter|LP|chrom&gene&filter&vkgl&exit_lp,G|missense_variant|MODERATE|NF1|4763|Transcript|NM_001042492.3|protein_coding|42/58||NM_001042492.3:c.6374T>G|NP_001035957.1:p.Leu2125Arg|6707/12373|6374/8520|2125/2839|L/R|cTg/cGg|CM141499&CM143458|1||1||1|EntrezGene|||||0|0.993||||1&1||||||||102|-42|41|-34|8|0.00|0.00|0.00|0.00|NF1|VUS|0.9962404||||||HP:0000951||0.583|1|AD||LP||||7.536000||||996527|Likely_pathogenic||criteria_provided&_single_submitter|LP|chrom&gene&filter&vkgl&exit_lp;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIG:VIM:VIPC_S:VIPP_S 1|0:25,25:50:50:AD_IP:0:4763:1:OK,OK:HR&GQ&DP&VIM&exit_ok,HR&GQ&DP&VIM&exit_ok 0|0:50,0:50:50:.:.:.:.:.:. 1|0:25,25:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.
121
121
  17 29683983 . C T . PASS CSQ=T|stop_gained|HIGH|NF1|4763|Transcript|NM_000267.3|protein_coding|52/57||NM_000267.3:c.7681C>T|NP_000258.1:p.Gln2561Ter|8064/12362|7681/8457|2561/2818|Q/*|Cag/Tag|CM143479|1||1|||EntrezGene||||||||||1|||||||||24|-5|24|36|0.02|0.00|0.00|0.00|NF1|VUS|0.9976593||||||HP:0000951||0.583|1|AD||LP||||6.871000||||||||LP|chrom&gene&filter&vkgl&exit_lp,T|stop_gained|HIGH|NF1|4763|Transcript|NM_001042492.3|protein_coding|53/58||NM_001042492.3:c.7744C>T|NP_001035957.1:p.Gln2582Ter|8077/12373|7744/8520|2582/2839|Q/*|Cag/Tag|CM143479|1||1||1|EntrezGene||||||||||1|||||||||24|-5|24|36|0.02|0.00|0.00|0.00|NF1|VUS|0.9986885||||||HP:0000951||0.583|1|AD||LP||||6.871000||||||||LP|chrom&gene&filter&vkgl&exit_lp;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIG:VIM:VIPC_S:VIPP_S:VIS .|.:25,25:50:50:AR,AD:0:4763:1:OK,OK:HR&GQ&DP&VIM&exit_ok,HR&GQ&DP&VIM&exit_ok:AR_C 0|0:50,0:50:50:.:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.:.
122
122
  19 11224051 . C CGTGGTCGCTCTGGACACGGAGCGTGGTCGCTCTGGACACGGAGCGTGGTCGCTCTGGACACGGAGCGTGGTCGCTCTGGACACGGAGCGTGGTCGCTCTGGACACGGAGCGTGGTCGCTCTGGACACGGAGCGTGGTCGCTCTGGACACGGAGCGTGGTCGCTCTGGACACGGAGCGTGGTCGCTCTGGACACGGAGCGTGGTCGCTCTGGACACGGAGCGTGGTCGCTCTGGACACGGAGCGTGGTCGCTCTGGACACGGAGCGTGGTCGCTCTGGACACGGAGCGTGGTCGCTCTGGACACGGAGCGTGGTCGCTCTGGACACGGAGCGTGGTCGCTCTGGACACGGAG . PASS CSQ=TCGCTCTGGACACGGAGGTGG|inframe_insertion|MODERATE|LDLR|3949|Transcript|NM_000527.5|protein_coding|9/18||NM_000527.5:c.1289_1309dup|NP_000518.1:p.Val436_Ala437insGlyGlyArgSerGlyHisGly|1395-1396/5173|1309-1310/2583|437/860|A/VALDTEVA|gcc/gTCGCTCTGGACACGGAGGTGGcc||1||1||1|EntrezGene|||||||25|||||||||||||||||||||VUS|0.8812568|||||||HC|5.497||AD&AR||LP||||||||||||LP|chrom&gene&filter&vkgl&exit_lp;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIG:VIM:VIPC_S:VIPP_S 1|1:.:10:50:AR:0:3949:1:OK:HR&GQ&DP&VIM&exit_ok 0|1:.:10:50:.:.:.:.:.:. 1|0:25,25:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.
123
123
  19 17449399 . C T . PASS CSQ=T|missense_variant|MODERATE|GTPBP3|84705|Transcript|NM_001128855.3|protein_coding|4/9||NM_001128855.3:c.440C>T|NP_001122327.1:p.Ala147Val|499/2503|440/1416|147/471|A/V|gCg/gTg|rs774708853&COSV50176281|1||1|||EntrezGene|||||0|0.999||likely_pathogenic|0&1|1&1||||||||64|-39|-47|-19|31|0.01|0.00|0.00|0.00|GTPBP3|VUS|0.92324424||||||HP:0000951||-1.926||AR||LP||||7.188000|19:17449399-17449399|7.96883e-06|0|488525|Conflicting_interpretations_of_pathogenicity||criteria_provided&_conflicting_interpretations|LP|chrom&gene&filter&vkgl&exit_lp,T|missense_variant|MODERATE|GTPBP3|84705|Transcript|NM_001195422.1|protein_coding|4/9||NM_001195422.1:c.506C>T|NP_001182351.1:p.Ala169Val|528/2595|506/1545|169/514|A/V|gCg/gTg|rs774708853&COSV50176281|1||1|||EntrezGene|||||0|0.997||likely_pathogenic|0&1|1&1||||||||64|-39|-47|-19|31|0.01|0.00|0.00|0.00|GTPBP3|VUS|0.65621275||||||HP:0000951||-1.926||AR||LP||||7.188000|19:17449399-17449399|7.96883e-06|0|488525|Conflicting_interpretations_of_pathogenicity||criteria_provided&_conflicting_interpretations|LP|chrom&gene&filter&vkgl&exit_lp,T|upstream_gene_variant|MODIFIER|ANO8|57719|Transcript|NM_020959.3|protein_coding||||||||||rs774708853&COSV50176281|1|3735|-1|||EntrezGene||||||||likely_pathogenic|0&1|1&1|||||||||-39|-47|-19|31|0.01|0.00|0.00|0.00|GTPBP3|VUS|0.71450377||||||||-1.785||||||||7.188000|19:17449399-17449399|7.96883e-06|0|488525|Conflicting_interpretations_of_pathogenicity||criteria_provided&_conflicting_interpretations|LP|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp,T|missense_variant|MODERATE|GTPBP3|84705|Transcript|NM_032620.4|protein_coding|4/9||NM_032620.4:c.440C>T|NP_116009.2:p.Ala147Val|499/2566|440/1479|147/492|A/V|gCg/gTg|rs774708853&COSV50176281|1||1|||EntrezGene|||||0|0.999||likely_pathogenic|0&1|1&1||||||||64|-39|-47|-19|31|0.01|0.00|0.00|0.00|GTPBP3|VUS|0.84315056||||||HP:0000951||-1.926||AR||LP||||7.188000|19:17449399-17449399|7.96883e-06|0|488525|Conflicting_interpretations_of_pathogenicity||criteria_provided&_conflicting_interpretations|LP|chrom&gene&filter&vkgl&exit_lp,T|missense_variant|MODERATE|GTPBP3|84705|Transcript|NM_133644.4|protein_coding|4/8||NM_133644.4:c.440C>T|NP_598399.2:p.Ala147Val|499/2662|440/1575|147/524|A/V|gCg/gTg|rs774708853&COSV50176281|1||1||1|EntrezGene|||||0|0.999||likely_pathogenic|0&1|1&1||||||||64|-39|-47|-19|31|0.01|0.00|0.00|0.00|GTPBP3|VUS|0.8864299||||||HP:0000951||-1.926||AR||LP||||7.188000|19:17449399-17449399|7.96883e-06|0|488525|Conflicting_interpretations_of_pathogenicity||criteria_provided&_conflicting_interpretations|LP|chrom&gene&filter&vkgl&exit_lp,T|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000107883|promoter||||||||||rs774708853&COSV50176281|1|||||||||||||likely_pathogenic|0&1|1&1|||||||||||||||||||||||||||||||||||7.188000|19:17449399-17449399|7.96883e-06|0|488525|Conflicting_interpretations_of_pathogenicity||criteria_provided&_conflicting_interpretations|LQ|chrom&gene&exit_rm;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIM:VIPC_S:VIPP_S 1|0:25,25:50:50:AD:1:0:OK,OK,OK,OK,OK,OK:HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok 0|0:50,0:50:50:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.
124
124
  19 17451997 . GA G . PASS CSQ=-|frameshift_variant|HIGH|GTPBP3|84705|Transcript|NM_001128855.3|protein_coding|8/9||NM_001128855.3:c.1058del|NP_001122327.1:p.Asn353ThrfsTer26|1117/2503|1058/1416|353/471|N/X|aAc/ac||1||1|||EntrezGene|||||||1||||||||||||34|33|-7|33|0.01|0.00|0.00|0.00|GTPBP3|VUS|0.99768054||||||HP:0000951||-1.926||AR||LP||||5.586000||||||||LP|chrom&gene&filter&vkgl&exit_lp,-|frameshift_variant|HIGH|GTPBP3|84705|Transcript|NM_001195422.1|protein_coding|8/9||NM_001195422.1:c.1187del|NP_001182351.1:p.Asn396ThrfsTer26|1209/2595|1187/1545|396/514|N/X|aAc/ac||1||1|||EntrezGene|||||||1||||||||||||34|33|-7|33|0.01|0.00|0.00|0.00|GTPBP3|VUS|0.99091107||||||HP:0000951||-1.926||AR||LP||||5.586000||||||||LP|chrom&gene&filter&vkgl&exit_lp,-|frameshift_variant|HIGH|GTPBP3|84705|Transcript|NM_032620.4|protein_coding|8/9||NM_032620.4:c.1121del|NP_116009.2:p.Asn374ThrfsTer26|1180/2566|1121/1479|374/492|N/X|aAc/ac||1||1|||EntrezGene|||||||1||||||||||||34|33|-7|33|0.01|0.00|0.00|0.00|GTPBP3|VUS|0.99607384||||||HP:0000951||-1.926||AR||LP||||5.586000||||||||LP|chrom&gene&filter&vkgl&exit_lp,-|frameshift_variant|HIGH|GTPBP3|84705|Transcript|NM_133644.4|protein_coding|7/8||NM_133644.4:c.1217del|NP_598399.2:p.Asn406ThrfsTer26|1276/2662|1217/1575|406/524|N/X|aAc/ac||1||1||1|EntrezGene|||||||1||||||||||||34|33|-7|33|0.01|0.00|0.00|0.00|GTPBP3|VUS|0.9972447||||||HP:0000951||-1.926||AR||LP||||5.586000||||||||LP|chrom&gene&filter&vkgl&exit_lp,-|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001610216|CTCF_binding_site|||||||||||1||||||||||||||||||||||||||||||||||||||||||||||||||5.586000||||||||LQ|chrom&gene&exit_rm,-|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001909308|promoter|||||||||||1||||||||||||||||||||||||||||||||||||||||||||||||||5.586000||||||||LQ|chrom&gene&exit_rm,-|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00523665928||||||||||||1||1||||||||||||||||ENSPFM0305|8|N||HOXB2::ELF1||||||||||||||||||||||||||||5.586000||||||||LQ|chrom&gene&exit_rm;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIG:VIM:VIPC_S:VIPP_S 1|1:0,50:50:50:AR:1:84705:1:OK,OK,OK,OK,OK,OK,OK:HR&GQ&DP&VIM&exit_ok,HR&GQ&DP&VIM&exit_ok,HR&GQ&DP&VIM&exit_ok,HR&GQ&DP&VIM&exit_ok,HR&GQ&DP&VIM&exit_ok,HR&GQ&DP&VIM&exit_ok,HR&GQ&DP&VIM&exit_ok 0|0:10,0:10:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 1|0:25,25:50:50:.:.:.:.:.:. 1|1:0,50:50:50:.:.:.:.:.:. 1|1:0,50:50:50:.:.:.:.:.:.
125
- 22 50721546 . C T . PASS CSQ=T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376864.1|protein_coding|17/37||NM_001376864.1:c.2749G>A|NP_001363793.1:p.Gly917Ser|2881/6611|2749/5754|917/1917|G/S|Ggc/Agc|rs1377653283|1||-1||1|EntrezGene||||||||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.14641568||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LB|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lb,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376865.1|protein_coding|18/38||NM_001376865.1:c.2818G>A|NP_001363794.1:p.Gly940Ser|2898/6391|2818/5586|940/1861|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene||||||||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.10027899||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LB|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lb,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376866.1|protein_coding|17/37||NM_001376866.1:c.2749G>A|NP_001363795.1:p.Gly917Ser|2909/6402|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.71265084||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376867.1|protein_coding|18/38||NM_001376867.1:c.2749G>A|NP_001363796.1:p.Gly917Ser|2969/6462|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.7664242||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376868.1|protein_coding|18/38||NM_001376868.1:c.2749G>A|NP_001363797.1:p.Gly917Ser|2962/6455|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.7664242||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376869.1|protein_coding|16/36||NM_001376869.1:c.2749G>A|NP_001363798.1:p.Gly917Ser|2856/6349|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.66974294||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376870.1|protein_coding|17/37||NM_001376870.1:c.2749G>A|NP_001363799.1:p.Gly917Ser|2881/6374|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.6837599||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376871.1|protein_coding|17/37||NM_001376871.1:c.2749G>A|NP_001363800.1:p.Gly917Ser|2874/6367|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.6837599||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376872.1|protein_coding|19/39||NM_001376872.1:c.2749G>A|NP_001363801.1:p.Gly917Ser|3066/6559|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.7025085||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376873.1|protein_coding|18/38||NM_001376873.1:c.2749G>A|NP_001363802.1:p.Gly917Ser|3218/6711|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.7267535||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376874.1|protein_coding|18/38||NM_001376874.1:c.2749G>A|NP_001363803.1:p.Gly917Ser|2934/6427|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.7664242||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376875.1|protein_coding|16/36||NM_001376875.1:c.2749G>A|NP_001363804.1:p.Gly917Ser|2933/6426|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.7664242||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376876.1|protein_coding|18/38||NM_001376876.1:c.2749G>A|NP_001363805.1:p.Gly917Ser|2927/6420|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.7664242||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376877.1|protein_coding|18/38||NM_001376877.1:c.2749G>A|NP_001363806.1:p.Gly917Ser|3198/6691|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.70509267||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376878.1|protein_coding|16/36||NM_001376878.1:c.2749G>A|NP_001363807.1:p.Gly917Ser|2821/6314|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.66974294||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376879.1|protein_coding|19/39||NM_001376879.1:c.2749G>A|NP_001363808.1:p.Gly917Ser|3101/6594|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.69429386||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376880.1|protein_coding|17/37||NM_001376880.1:c.2749G>A|NP_001363809.1:p.Gly917Ser|2991/6484|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.7664242||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376881.1|protein_coding|18/38||NM_001376881.1:c.2749G>A|NP_001363810.1:p.Gly917Ser|3046/6539|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.8251113||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376882.1|protein_coding|17/37||NM_001376882.1:c.2749G>A|NP_001363811.1:p.Gly917Ser|3165/6658|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.70509267||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376883.1|protein_coding|17/37||NM_001376883.1:c.2749G>A|NP_001363812.1:p.Gly917Ser|2881/6350|2749/5493|917/1830|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene||||||||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.10285367||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LB|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lb,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376884.1|protein_coding|16/36||NM_001376884.1:c.2749G>A|NP_001363813.1:p.Gly917Ser|2821/6236|2749/5439|917/1812|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene||||||||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.119815774||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LB|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lb,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376885.1|protein_coding|17/37||NM_001376885.1:c.2749G>A|NP_001363814.1:p.Gly917Ser|2909/6324|2749/5439|917/1812|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene||||||||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.114952855||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LB|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lb,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376886.1|protein_coding|17/37||NM_001376886.1:c.2656G>A|NP_001363815.1:p.Gly886Ser|2876/6369|2656/5424|886/1807|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene||||||||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.12163515||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LB|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lb,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_012401.4|protein_coding|17/37||NM_012401.4:c.2749G>A|NP_036533.2:p.Gly917Ser|2916/6409|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.75893486||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp,T|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001960812|promoter||||||||||rs1377653283|1||||||||||||||||||||||||||||||||||||||||||||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LQ|chrom&gene&exit_rm;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIM:VIPC_S:VIPP_S 1|1:0,50:50:50:AR:1:0:OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK:HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok 0|0:10,0:10:50:.:.:.:.:. 1|0:25,25:50:50:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:. 1|0:25,25:50:50:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.
125
+ 22 50721546 . C T . PASS CSQ=T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376864.1|protein_coding|17/37||NM_001376864.1:c.2749G>A|NP_001363793.1:p.Gly917Ser|2881/6611|2749/5754|917/1917|G/S|Ggc/Agc|rs1377653283|1||-1||1|EntrezGene||||||||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.14641568||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LB|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lb,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376865.1|protein_coding|18/38||NM_001376865.1:c.2818G>A|NP_001363794.1:p.Gly940Ser|2898/6391|2818/5586|940/1861|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene||||||||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.10027899||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LB|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lb,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376866.1|protein_coding|17/37||NM_001376866.1:c.2749G>A|NP_001363795.1:p.Gly917Ser|2909/6402|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.71265084||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376867.1|protein_coding|18/38||NM_001376867.1:c.2749G>A|NP_001363796.1:p.Gly917Ser|2969/6462|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.7664242||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376868.1|protein_coding|18/38||NM_001376868.1:c.2749G>A|NP_001363797.1:p.Gly917Ser|2962/6455|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.7664242||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376869.1|protein_coding|16/36||NM_001376869.1:c.2749G>A|NP_001363798.1:p.Gly917Ser|2856/6349|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.66974294||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376870.1|protein_coding|17/37||NM_001376870.1:c.2749G>A|NP_001363799.1:p.Gly917Ser|2881/6374|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.6837599||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376871.1|protein_coding|17/37||NM_001376871.1:c.2749G>A|NP_001363800.1:p.Gly917Ser|2874/6367|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.6837599||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376872.1|protein_coding|19/39||NM_001376872.1:c.2749G>A|NP_001363801.1:p.Gly917Ser|3066/6559|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.7025085||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376873.1|protein_coding|18/38||NM_001376873.1:c.2749G>A|NP_001363802.1:p.Gly917Ser|3218/6711|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.7267535||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376874.1|protein_coding|18/38||NM_001376874.1:c.2749G>A|NP_001363803.1:p.Gly917Ser|2934/6427|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.7664242||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376875.1|protein_coding|16/36||NM_001376875.1:c.2749G>A|NP_001363804.1:p.Gly917Ser|2933/6426|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.7664242||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376876.1|protein_coding|18/38||NM_001376876.1:c.2749G>A|NP_001363805.1:p.Gly917Ser|2927/6420|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.7664242||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376877.1|protein_coding|18/38||NM_001376877.1:c.2749G>A|NP_001363806.1:p.Gly917Ser|3198/6691|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.70509267||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376878.1|protein_coding|16/36||NM_001376878.1:c.2749G>A|NP_001363807.1:p.Gly917Ser|2821/6314|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.66974294||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376879.1|protein_coding|19/39||NM_001376879.1:c.2749G>A|NP_001363808.1:p.Gly917Ser|3101/6594|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.69429386||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376880.1|protein_coding|17/37||NM_001376880.1:c.2749G>A|NP_001363809.1:p.Gly917Ser|2991/6484|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.7664242||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376881.1|protein_coding|18/38||NM_001376881.1:c.2749G>A|NP_001363810.1:p.Gly917Ser|3046/6539|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.8251113||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376882.1|protein_coding|17/37||NM_001376882.1:c.2749G>A|NP_001363811.1:p.Gly917Ser|3165/6658|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.70509267||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376883.1|protein_coding|17/37||NM_001376883.1:c.2749G>A|NP_001363812.1:p.Gly917Ser|2881/6350|2749/5493|917/1830|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene||||||||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.10285367||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LB|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lb,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376884.1|protein_coding|16/36||NM_001376884.1:c.2749G>A|NP_001363813.1:p.Gly917Ser|2821/6236|2749/5439|917/1812|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene||||||||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.119815774||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LB|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lb,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376885.1|protein_coding|17/37||NM_001376885.1:c.2749G>A|NP_001363814.1:p.Gly917Ser|2909/6324|2749/5439|917/1812|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene||||||||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.114952855||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LB|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lb,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_001376886.1|protein_coding|17/37||NM_001376886.1:c.2656G>A|NP_001363815.1:p.Gly886Ser|2876/6369|2656/5424|886/1807|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene||||||||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.12163515||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LB|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lb,T|missense_variant|MODERATE|PLXNB2|23654|Transcript|NM_012401.4|protein_coding|17/37||NM_012401.4:c.2749G>A|NP_036533.2:p.Gly917Ser|2916/6409|2749/5517|917/1838|G/S|Ggc/Agc|rs1377653283|1||-1|||EntrezGene|||||0|1||||||||||||56|-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.75893486||||||||0.546||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LP|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp,T|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001960812|promoter||||||||||rs1377653283|1||||||||||||||||||||||||||||||||||||||||||||||||||6.433000|22:50721546-50721546|4.49665e-06|0|||||LQ|chrom&gene&exit_rm;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIM:VIPC_S:VIPP_S 1|1:0,50:50:50:AR:.:0:OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK:HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok 0|0:10,0:10:50:.:.:.:.:. 1|0:25,25:50:50:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:. 1|0:25,25:50:50:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.
126
+ 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|chrom&gene&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:HR&VIM&exit_ok 1|0:45,5:.:.:.:.:.:. 0|0:50,0:.:.:.:.:.:. 1|0:25,25:.:.:.:.:.:. 0|0:50,0:.:.:.:.:.:. 0|0:50,0:.:.:.:.:.:.
126
127
  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|chrom&gene&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|chrom&gene&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|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&exit_lp,T|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001477865|CTCF_binding_site||||||||||CS135341|1|||||||||||||||1|||||||||||||||||||||||||||||||||||8.134000||||||||LQ|chrom&gene&exit_rm,T|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001765299|promoter_flanking_region||||||||||CS135341|1|||||||||||||||1|||||||||||||||||||||||||||||||||||8.134000||||||||LQ|chrom&gene&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:HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok 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:.:.:.:.
127
128
  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|chrom&gene&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:HR&GQ&DP&VIM&VID&exit_ok 0:.:10:50:.:.:.:. .:.:.:50:.:.:.:. .:.:.:50:.:.:.:. 1:50:50:50:.:.:.:. 1:50:50:50:.:.:.:.
package/src/views/SampleVariants.tsx CHANGED
@@ -158,9 +158,24 @@ export const SampleVariants: Component<{
158
158
  actions.setSampleVariantsFilterQuery(
159
159
  props.sample,
160
160
  {
161
- selector: selectorGq,
162
- operator: ">=",
163
- args: 20,
161
+ operator: "or",
162
+ args: [
163
+ {
164
+ selector: selectorGq,
165
+ operator: ">=",
166
+ args: 20,
167
+ },
168
+ {
169
+ selector: selectorGq,
170
+ operator: "==",
171
+ args: null,
172
+ },
173
+ {
174
+ selector: selectorGq,
175
+ operator: "==",
176
+ args: undefined,
177
+ },
178
+ ],
164
179
  },
165
180
  selectorKey(selectorGq),
166
181
  );
@@ -173,6 +188,19 @@ export const SampleVariants: Component<{
173
188
  selectorKey(["s", props.sample.data.index, ...selector(viabField)]),
174
189
  );
175
190
  }
191
+ const viField = props.recordsMeta.format?.VI;
192
+ if (viField) {
193
+ const selectorVi = sampleSelector(props.sample, viField);
194
+ actions.setSampleVariantsFilterQuery(
195
+ props.sample,
196
+ {
197
+ selector: selectorVi,
198
+ operator: "has_any",
199
+ args: ["AD", "AR", "AR_C", "XLD", "XLR"],
200
+ },
201
+ selectorKey(selectorVi),
202
+ );
203
+ }
176
204
  }
177
205
 
178
206
  if (getStateVariants()?.sort === undefined) {
@@ -213,12 +241,31 @@ export const SampleVariants: Component<{
213
241
 
214
242
  const formatFields = createMemo(() => {
215
243
  const formatFieldMap = props.recordsMeta.format;
216
- const includedFields = ["VIM", "VID", "GQ", "VIAB", "GT", "DP"];
244
+ const includedFields = ["VIM", "VID", "VI", "GQ", "VIAB", "GT", "DP"];
217
245
  return formatFieldMap
218
246
  ? includedFields.map((fieldId) => formatFieldMap[fieldId]).filter((field) => field !== undefined)
219
247
  : [];
220
248
  });
221
249
 
250
+ const filterInfoFields = createMemo(() => {
251
+ const csqNestedFields = props.recordsMeta.info.CSQ?.nested?.items;
252
+ const includedFields = [];
253
+ const additionalCsqFieldsIds = ["IncompletePenetrance"];
254
+ const filterInfoFieldsIds = ["SVTYPE"];
255
+ const additionalCsqFields = csqNestedFields
256
+ ? (additionalCsqFieldsIds
257
+ .map((fieldId) => csqNestedFields.find((field) => field.id === fieldId))
258
+ .filter((field) => field !== undefined) as FieldMetadata[])
259
+ : [];
260
+ const filterInfoFields = filterInfoFieldsIds
261
+ .map((fieldId) => props.recordsMeta.info[fieldId])
262
+ .filter((field) => field !== undefined);
263
+ includedFields.push(...infoFields());
264
+ includedFields.push(...additionalCsqFields);
265
+ includedFields.push(...filterInfoFields);
266
+ return includedFields;
267
+ });
268
+
222
269
  const page = () => getStateVariants()?.page;
223
270
  const pageSize = () => getStateVariants()?.pageSize;
224
271
  const searchQuery = () => getStateVariants()?.searchQuery;
@@ -269,7 +316,7 @@ export const SampleVariants: Component<{
269
316
  <div class="column is-1-fullhd is-2">
270
317
  <SearchBox value={searchQuery()} onInput={onSearchChange} />
271
318
  <Filters
272
- fields={infoFields()}
319
+ fields={filterInfoFields()}
273
320
  samplesFields={[{ sample: props.sample, fields: formatFields() }]}
274
321
  queries={filterQueries()}
275
322
  onChange={onFilterChange}
package/src/views/data/SampleData.tsx CHANGED
@@ -3,9 +3,11 @@ import { RouteDataFuncArgs } from "@solidjs/router/dist/types";
3
3
  import { EMPTY_SAMPLE_ITEM, fetchSampleById } from "../../utils/ApiUtils";
4
4
  import { Item, Sample } from "@molgenis/vip-report-api/src/Api";
5
5
 
6
+ export type SampleParams = { sampleId: string };
6
7
  export type SampleRouteData = { sample: Resource<Item<Sample>> };
7
8
 
8
9
  export default function SampleData({ params }: RouteDataFuncArgs): SampleRouteData {
10
+ // eslint-disable-next-line @typescript-eslint/no-unsafe-return, @typescript-eslint/no-unsafe-member-access
9
11
  const [sample] = createResource(() => params.sampleId, fetchSampleById, { initialValue: EMPTY_SAMPLE_ITEM });
10
12
  return { sample };
11
13
  }
package/src/views/data/SampleVariantConsequenceData.tsx CHANGED
@@ -7,6 +7,7 @@ export default function SampleVariantConsequenceData({
7
7
  params,
8
8
  data,
9
9
  }: RouteDataFuncArgs): SampleVariantConsequenceRouteData {
10
+ // eslint-disable-next-line @typescript-eslint/no-unsafe-return, @typescript-eslint/no-unsafe-member-access, @typescript-eslint/no-unsafe-argument
10
11
  const consequenceId: number = parseInt(params.consequenceId);
11
12
  return { ...(data as SampleVariantRouteData), consequenceId };
12
13
  }
package/src/views/data/SampleVariantData.tsx CHANGED
@@ -8,6 +8,7 @@ import { Record } from "@molgenis/vip-report-vcf/src/Vcf";
8
8
  export type SampleVariantRouteData = SampleRouteData & { variant: Resource<Item<Record> | undefined> };
9
9
 
10
10
  export default function SampleVariantData({ params, data }: RouteDataFuncArgs): SampleVariantRouteData {
11
+ // eslint-disable-next-line @typescript-eslint/no-unsafe-return, @typescript-eslint/no-unsafe-member-access
11
12
  const [variant] = createResource(() => params.variantId, fetchRecordById);
12
13
  return { ...(data as SampleRouteData), variant };
13
14
  }
package/src/views/data/VariantConsequenceData.tsx CHANGED
@@ -4,6 +4,7 @@ import { VariantRouteData } from "./VariantData";
4
4
  export type VariantConsequenceRouteData = { consequenceId: number } & VariantRouteData;
5
5
 
6
6
  export default function VariantConsequenceData({ params, data }: RouteDataFuncArgs): VariantConsequenceRouteData {
7
+ // eslint-disable-next-line @typescript-eslint/no-unsafe-return, @typescript-eslint/no-unsafe-member-access, @typescript-eslint/no-unsafe-argument
7
8
  const consequenceId: number = parseInt(params.consequenceId);
8
9
  return { ...(data as VariantRouteData), consequenceId };
9
10
  }
package/src/views/data/VariantData.tsx CHANGED
@@ -7,6 +7,7 @@ import { Record } from "@molgenis/vip-report-vcf/src/Vcf";
7
7
  export type VariantRouteData = { variant: Resource<Item<Record>> };
8
8
 
9
9
  export default function VariantData({ params }: RouteDataFuncArgs): VariantRouteData {
10
+ // eslint-disable-next-line @typescript-eslint/no-unsafe-return, @typescript-eslint/no-unsafe-member-access
10
11
  const [variant] = createResource(() => params.variantId, fetchRecordById, { initialValue: EMPTY_RECORD_ITEM });
11
12
  return { variant };
12
13
  }
package/tsconfig.json CHANGED
@@ -3,7 +3,7 @@
3
3
  "strict": true,
4
4
  "target": "ESNext",
5
5
  "module": "ESNext",
6
- "moduleResolution": "node",
6
+ "moduleResolution": "bundler",
7
7
  "allowSyntheticDefaultImports": true,
8
8
  "esModuleInterop": true,
9
9
  "jsx": "preserve",
package/{vite.config.ts → vite.config.mts} RENAMED
@@ -1,6 +1,6 @@
1
1
  import { defineConfig } from "vitest/config";
2
2
  import solidPlugin from "vite-plugin-solid";
3
- import inlinePlugin from "@molgenis/vite-plugin-inline/src/vite-plugin-inline.js";
3
+ import inlinePlugin from "@molgenis/vite-plugin-inline";
4
4
 
5
5
  export default defineConfig({
6
6
  plugins: [solidPlugin(), inlinePlugin()],
@@ -12,7 +12,7 @@ export default defineConfig({
12
12
  polyfillDynamicImport: false,
13
13
  // inline plugin build options
14
14
  rollupOptions: {
15
- input: ["./index.html", "@molgenis/vite-plugin-inline/src/loader.ts"],
15
+ input: ["./index.html", "./node_modules/@molgenis/vite-plugin-inline/dist/loader.js"],
16
16
  output: {
17
17
  manualChunks: undefined,
18
18
  },