@molgenis/vip-report-template 5.4.1 → 5.5.2

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Files changed (8) hide show
  1. package/package.json +3 -3
  2. package/src/components/filter/Filter.tsx +4 -0
  3. package/src/components/filter/FilterHpo.tsx +153 -0
  4. package/src/components/filter/InfoFilter.tsx +20 -5
  5. package/src/components/record/info/Hpo.tsx +20 -4
  6. package/src/index.tsx +14 -1
  7. package/src/mocks/GRCh37/vcf/family.vcf.blob +51 -35
  8. package/src/views/SampleVariants.tsx +26 -3
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@molgenis/vip-report-template",
3
- "version": "5.4.1",
3
+ "version": "5.5.2",
4
4
  "description": "Report Template for Variant Call Format (VCF) Report Generator",
5
5
  "scripts": {
6
6
  "build": "vite build",
@@ -36,8 +36,8 @@
36
36
  "dependencies": {
37
37
  "@fortawesome/fontawesome-svg-core": "^6.4.0",
38
38
  "@fortawesome/free-solid-svg-icons": "^6.4.0",
39
- "@molgenis/vip-report-api": "^4.4.1",
40
- "@molgenis/vip-report-vcf": "^1.4.1",
39
+ "@molgenis/vip-report-api": "^4.4.2",
40
+ "@molgenis/vip-report-vcf": "^1.4.2",
41
41
  "@solidjs/router": "^0.8.2",
42
42
  "base64-js": "^1.5.1",
43
43
  "igv": "^2.15.8",
package/src/components/filter/Filter.tsx CHANGED
@@ -10,6 +10,7 @@ import { FilterClinVar } from "./FilterClinVar";
10
10
  import { isAnyCsqInfo } from "../../utils/csqUtils";
11
11
  import { FilterChangeEvent, FilterClearEvent } from "./Filters";
12
12
  import { FilterAllelicBalance } from "./FilterAllelicBalance";
13
+ import { FilterHpo } from "./FilterHpo";
13
14
 
14
15
  export type FilterProps = {
15
16
  field: FieldMetadata;
@@ -41,6 +42,9 @@ export const Filter: Component<FilterProps> = (props) => {
41
42
  <Match when={isAnyCsqInfo(props.field, ["clinVar_CLNSIG", "clinVar_CLNSIGINCL"])}>
42
43
  <FilterClinVar {...props} />
43
44
  </Match>
45
+ <Match when={props.field.id === "HPO"}>
46
+ <FilterHpo {...props} />
47
+ </Match>
44
48
  <Match when={props.field.type === "CATEGORICAL"}>
45
49
  <FilterCategorical {...props} />
46
50
  </Match>
package/src/components/filter/FilterHpo.tsx ADDED
@@ -0,0 +1,153 @@
1
+ import { Component, For, Show } from "solid-js";
2
+ import { Checkbox, CheckboxEvent } from "../Checkbox";
3
+ import { FilterProps } from "./Filter";
4
+ import { infoSelector, selector, selectorKey } from "../../utils/query";
5
+ import { FieldMetadata } from "@molgenis/vip-report-vcf/src/MetadataParser";
6
+ import { Query, QueryClause } from "@molgenis/vip-report-api/src/Api";
7
+
8
+ export type CheckboxGroup = {
9
+ [key: string]: boolean;
10
+ };
11
+
12
+ export type CategoryLabels = {
13
+ [key: string]: string;
14
+ };
15
+
16
+ export const FilterHpo: Component<
17
+ FilterProps & {
18
+ labels?: CategoryLabels;
19
+ }
20
+ > = (props) => {
21
+ const group: CheckboxGroup = {};
22
+ const hpoSelector = selector(props.field);
23
+ const csqMeta = props.field.parent;
24
+ let gadoHcChecked = false;
25
+ let gadoLcChecked = false;
26
+ let hpoValues: (string | null)[] = [];
27
+
28
+ let gadoMeta: FieldMetadata | null = null;
29
+ csqMeta?.nested?.items.forEach((meta) => {
30
+ if (meta.id === "GADO_PD") {
31
+ gadoMeta = meta;
32
+ }
33
+ });
34
+
35
+ if (props.query !== undefined) {
36
+ (props.query.args as Query[]).forEach((childQuery) => {
37
+ if (selectorKey((childQuery as QueryClause).selector) === selectorKey(infoSelector(props.field))) {
38
+ (childQuery.args as string[]).forEach((key) => {
39
+ group[key] = true;
40
+ hpoValues.push(key);
41
+ });
42
+ } else if (
43
+ gadoMeta &&
44
+ selectorKey((childQuery as QueryClause).selector) === selectorKey(infoSelector(gadoMeta))
45
+ ) {
46
+ if ((childQuery.args as string[]).indexOf("LC") !== -1) {
47
+ gadoLcChecked = true;
48
+ }
49
+ if ((childQuery.args as string[]).indexOf("HC") !== -1) {
50
+ gadoHcChecked = true;
51
+ }
52
+ }
53
+ });
54
+ }
55
+
56
+ const nullValue = "__null";
57
+
58
+ let gadoLcQuery: Query;
59
+ let gadoHcQuery: Query;
60
+ if (gadoMeta !== null) {
61
+ gadoLcQuery = {
62
+ selector: selector(gadoMeta),
63
+ operator: "has_any",
64
+ args: ["LC"],
65
+ };
66
+
67
+ gadoHcQuery = {
68
+ selector: selector(gadoMeta),
69
+ operator: "has_any",
70
+ args: ["HC"],
71
+ };
72
+ }
73
+ const onChange = (event: CheckboxEvent) => {
74
+ const queries: Query[] = [];
75
+ group[event.value !== undefined ? event.value : nullValue] = event.checked;
76
+ const values = Object.keys(group)
77
+ .filter((key) => group[key])
78
+ .map((key) => (key !== nullValue ? key : null));
79
+ if (values.length > 0) {
80
+ if (gadoMeta !== null) {
81
+ if (values.includes("gado_lc")) {
82
+ queries.push(gadoLcQuery);
83
+ gadoLcChecked = true;
84
+ } else {
85
+ gadoHcChecked = false;
86
+ }
87
+ if (values.includes("gado_hc")) {
88
+ queries.push(gadoHcQuery);
89
+ gadoHcChecked = true;
90
+ } else {
91
+ gadoHcChecked = false;
92
+ }
93
+ }
94
+ hpoValues = values.filter((key) => key !== "gado_lc" && key !== "gado_hc");
95
+ if (hpoValues.length > 0) {
96
+ const hpoQuery: Query = {
97
+ selector: hpoSelector,
98
+ operator: "any_has_any",
99
+ args: hpoValues,
100
+ };
101
+ queries.push(hpoQuery);
102
+ } else if (gadoMeta !== null) {
103
+ props.onClear({ key: selectorKey(hpoSelector) });
104
+ }
105
+
106
+ props.onChange({
107
+ key: selectorKey(hpoSelector),
108
+ query: {
109
+ operator: "or",
110
+ args: queries,
111
+ },
112
+ });
113
+ } else {
114
+ props.onClear({ key: selectorKey(hpoSelector) });
115
+ }
116
+ };
117
+ return (
118
+ <>
119
+ <For each={props.field.categories}>
120
+ {(category) => (
121
+ <div class="control">
122
+ <Checkbox
123
+ value={category}
124
+ label={props.labels ? props.labels[category] : category}
125
+ checked={hpoValues && hpoValues.includes(category)}
126
+ onChange={onChange}
127
+ />
128
+ </div>
129
+ )}
130
+ </For>
131
+ <Show when={gadoMeta !== null}>
132
+ <div class="control">
133
+ <Checkbox
134
+ value="gado_hc"
135
+ label="GADO high"
136
+ 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)."
137
+ checked={gadoHcChecked}
138
+ onChange={onChange}
139
+ />
140
+ </div>
141
+ <div class="control">
142
+ <Checkbox
143
+ value="gado_lc"
144
+ label="GADO low"
145
+ 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)."
146
+ checked={gadoLcChecked}
147
+ onChange={onChange}
148
+ />
149
+ </div>
150
+ </Show>
151
+ </>
152
+ );
153
+ };
package/src/components/filter/InfoFilter.tsx CHANGED
@@ -1,7 +1,7 @@
1
1
  import { Component } from "solid-js";
2
2
  import { Filter, FilterProps } from "./Filter";
3
3
  import { FilterChangeEvent, FilterClearEvent } from "./Filters";
4
- import { QueryClause, SelectorPart } from "@molgenis/vip-report-api/src/Api";
4
+ import { ComposedQuery, Query, QueryClause, SelectorPart } from "@molgenis/vip-report-api/src/Api";
5
5
  import { selectorKey } from "../../utils/query";
6
6
 
7
7
  export const InfoFilter: Component<FilterProps> = (props) => {
@@ -10,13 +10,28 @@ export const InfoFilter: Component<FilterProps> = (props) => {
10
10
  const onChange = (event: FilterChangeEvent) => {
11
11
  props.onChange({
12
12
  key: selectorKey(["n", event.key]),
13
- query: {
14
- ...(event.query as QueryClause),
15
- selector: ["n", ...((event.query as QueryClause).selector as SelectorPart[])],
16
- },
13
+ query: updateQuery(event.query),
17
14
  });
18
15
  };
19
16
 
17
+ function updateQuery(query: Query): QueryClause | ComposedQuery {
18
+ let updatedQuery: QueryClause | ComposedQuery;
19
+ if ((query as QueryClause).selector !== undefined) {
20
+ updatedQuery = {
21
+ ...(query as QueryClause),
22
+ selector: ["n", ...((query as QueryClause).selector as SelectorPart[])],
23
+ };
24
+ } else {
25
+ const queries: (QueryClause | ComposedQuery)[] = [];
26
+ (query as ComposedQuery).args.forEach((subQuery) => queries.push(updateQuery(subQuery)));
27
+ updatedQuery = {
28
+ operator: (query as ComposedQuery).operator,
29
+ args: queries,
30
+ };
31
+ }
32
+ return updatedQuery;
33
+ }
34
+
20
35
  const onClear = (event: FilterClearEvent) => {
21
36
  props.onClear({
22
37
  key: selectorKey(["n", event.key]),
package/src/components/record/info/Hpo.tsx CHANGED
@@ -1,10 +1,7 @@
1
- import { Component, createMemo, For, Show } from "solid-js";
1
+ import { Component, For, Show } from "solid-js";
2
2
  import { Anchor } from "../../Anchor";
3
3
  import { FieldProps } from "../field/Field";
4
- import { ValueFlag, ValueString } from "@molgenis/vip-report-vcf/src/ValueParser";
5
4
  import { getCsqInfo, getCsqInfoIndex } from "../../../utils/csqUtils";
6
- import { Abbr } from "../../Abbr";
7
- import { FieldSingleValue } from "../field/FieldSingleValue";
8
5
  import { FieldValueString } from "../field/FieldValueString";
9
6
 
10
7
  type HpoTerm = {
@@ -19,6 +16,9 @@ export const Hpo: Component<FieldProps> = (props) => {
19
16
  href: `https://hpo.jax.org/app/browse/term/${encodeURI(hpoTermId)}`,
20
17
  }));
21
18
 
19
+ const gadoIndex = (): number => getCsqInfoIndex(props.infoMeta, "GADO_PD");
20
+ const gadoClass = (): string | null => (gadoIndex() !== -1 ? (getCsqInfo(props.info, gadoIndex()) as string) : null);
21
+
22
22
  return (
23
23
  <>
24
24
  <For each={hpoTerms()}>
@@ -31,6 +31,22 @@ export const Hpo: Component<FieldProps> = (props) => {
31
31
  </>
32
32
  )}
33
33
  </For>
34
+ <Show when={gadoClass() !== null && gadoClass() === "LC"} keyed>
35
+ <abbr
36
+ title="Gene phenotype relation predicted by GADO with low confidence; Z-Score greater than 3 but below 5."
37
+ class="ml-1 is-clickable"
38
+ >
39
+ <i class="fas fa-question-circle has-text-info" />
40
+ </abbr>
41
+ </Show>
42
+ <Show when={gadoClass() !== null && gadoClass() === "HC"} keyed>
43
+ <abbr
44
+ title="Gene phenotype relation predicted by GADO with high confidence; Z-Score greater than 5."
45
+ class="ml-1 is-clickable"
46
+ >
47
+ <i class="fas fa-info-circle has-text-info" />
48
+ </abbr>
49
+ </Show>
34
50
  </>
35
51
  );
36
52
  };
package/src/index.tsx CHANGED
@@ -10,6 +10,8 @@ import {
10
10
  faAngleUp,
11
11
  faCircleExclamation,
12
12
  faCircleXmark,
13
+ faCircleInfo,
14
+ faCircleQuestion,
13
15
  faDownload,
14
16
  faExternalLink,
15
17
  faHome,
@@ -17,7 +19,18 @@ import {
17
19
  } from "@fortawesome/free-solid-svg-icons";
18
20
  import { Provider } from "./store";
19
21
 
20
- library.add(faAngleDown, faAngleUp, faCircleExclamation, faCircleXmark, faDownload, faExternalLink, faHome, faSearch);
22
+ library.add(
23
+ faAngleDown,
24
+ faAngleUp,
25
+ faCircleExclamation,
26
+ faCircleXmark,
27
+ faCircleInfo,
28
+ faCircleQuestion,
29
+ faDownload,
30
+ faExternalLink,
31
+ faHome,
32
+ faSearch
33
+ );
21
34
 
22
35
  function processIcons() {
23
36
  void dom.i2svg();
package/src/mocks/GRCh37/vcf/family.vcf.blob CHANGED
@@ -8,21 +8,29 @@
8
8
  ##CAPICE_SC=CAPICE score
9
9
  ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
10
10
  ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
11
- ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
12
11
  ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
12
+ ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
13
13
  ##FORMAT=<ID=VI,Number=.,Type=String,Description="An enumeration of possible inheritance modes.">
14
14
  ##FORMAT=<ID=VIC,Number=1,Type=String,Description="Possible Compound hetrozygote variants.">
15
15
  ##FORMAT=<ID=VID,Number=1,Type=Integer,Description="Inheritance Denovo status.">
16
16
  ##FORMAT=<ID=VIG,Number=.,Type=String,Description="Genes with an inheritance match.">
17
17
  ##FORMAT=<ID=VIM,Number=1,Type=Integer,Description="Inheritance Match status.">
18
+ ##FORMAT=<ID=VIPC_S,Number=.,Type=String,Description="VIP decision tree classification.">
19
+ ##FORMAT=<ID=VIPP_S,Number=.,Type=String,Description="VIP decision tree path.">
18
20
  ##FORMAT=<ID=VIS,Number=.,Type=String,Description="An enumeration of possible sub inheritance modes like e.g. compound, non penetrance.">
21
+ ##GADO_PD=The GADO prediction for the relation between the phenotypes and the gene, HC: high confidence, LC: low confidence.
22
+ ##GADO_SC=The combined prioritization GADO Z-score over the supplied HPO terms for this case.
23
+ ##Grantham=Grantham Matrix score - Grantham, R. Amino Acid Difference Formula to Help Explain Protein Evolution, Science 1974 Sep 6;185(4154):862-4.
19
24
  ##HPO=List of HPO terms for the gene
20
25
  ##INFO=<ID=BND_DEPTH,Number=1,Type=Integer,Description="Read depth at local translocation breakend">
21
- ##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|ALLELE_NUM|DISTANCE|STRAND|FLAGS|PICK|SYMBOL_SOURCE|HGNC_ID|REFSEQ_MATCH|REFSEQ_OFFSET|SOURCE|SIFT|PolyPhen|HGVS_OFFSET|CLIN_SIG|SOMATIC|PHENO|PUBMED|CHECK_REF|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|TRANSCRIPTION_FACTORS|SpliceAI_pred_DP_AG|SpliceAI_pred_DP_AL|SpliceAI_pred_DP_DG|SpliceAI_pred_DP_DL|SpliceAI_pred_DS_AG|SpliceAI_pred_DS_AL|SpliceAI_pred_DS_DG|SpliceAI_pred_DS_DL|SpliceAI_pred_SYMBOL|CAPICE_CL|CAPICE_SC|HPO|IncompletePenetrance|InheritanceModesGene|VKGL_CL|ASV_ACMG_class|ASV_AnnotSV_ranking_criteria|ASV_AnnotSV_ranking_score|gnomAD|gnomAD_AF|gnomAD_HN|clinVar|clinVar_CLNSIG|clinVar_CLNSIGINCL|clinVar_CLNREVSTAT|VIPC|VIPP|VIPL">
26
+ ##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|ALLELE_NUM|DISTANCE|STRAND|FLAGS|PICK|SYMBOL_SOURCE|HGNC_ID|REFSEQ_MATCH|REFSEQ_OFFSET|SOURCE|SIFT|PolyPhen|HGVS_OFFSET|CLIN_SIG|SOMATIC|PHENO|PUBMED|CHECK_REF|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|TRANSCRIPTION_FACTORS|Grantham|SpliceAI_pred_DP_AG|SpliceAI_pred_DP_AL|SpliceAI_pred_DP_DG|SpliceAI_pred_DP_DL|SpliceAI_pred_DS_AG|SpliceAI_pred_DS_AL|SpliceAI_pred_DS_DG|SpliceAI_pred_DS_DL|SpliceAI_pred_SYMBOL|CAPICE_CL|CAPICE_SC|existing_InFrame_oORFs|existing_OutOfFrame_oORFs|existing_uORFs|five_prime_UTR_variant_annotation|five_prime_UTR_variant_consequence|HPO|GADO_PD|GADO_SC|IncompletePenetrance|InheritanceModesGene|VKGL|VKGL_CL|ASV_ACMG_class|ASV_AnnotSV_ranking_criteria|ASV_AnnotSV_ranking_score|phyloP|gnomAD|gnomAD_AF|gnomAD_HN|clinVar|clinVar_CLNSIG|clinVar_CLNSIGINCL|clinVar_CLNREVSTAT|VIPC|VIPP">
27
+ ##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
28
+ ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
22
29
  ##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakend">
23
30
  ##INFO=<ID=MATE_BND_DEPTH,Number=1,Type=Integer,Description="Read depth at remote translocation mate breakend">
24
31
  ##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
25
32
  ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
33
+ ##INFO=<ID=VIPC_S,Number=.,Type=String,Description="VIP decision tree classification (samples).">
26
34
  ##INFO=<ID=clinVar,Number=.,Type=String,Description="/groups/solve-rd/tmp10/projects/vip/git/vip/resources/GRCh37/clinvar_20220620.vcf.gz (exact)">
27
35
  ##INFO=<ID=clinVar_CLNREVSTAT,Number=.,Type=String,Description="CLNREVSTAT field from /groups/solve-rd/tmp10/projects/vip/git/vip/resources/GRCh37/clinvar_20220620.vcf.gz">
28
36
  ##INFO=<ID=clinVar_CLNSIG,Number=.,Type=String,Description="CLNSIG field from /groups/solve-rd/tmp10/projects/vip/git/vip/resources/GRCh37/clinvar_20220620.vcf.gz">
@@ -30,9 +38,7 @@
30
38
  ##INFO=<ID=gnomAD,Number=.,Type=String,Description="/groups/solve-rd/tmp10/projects/vip/git/vip/resources/GRCh37/gnomad.total.r2.1.1.sites.stripped.vcf.gz (exact)">
31
39
  ##INFO=<ID=gnomAD_AF,Number=.,Type=String,Description="AF field from /groups/solve-rd/tmp10/projects/vip/git/vip/resources/GRCh37/gnomad.total.r2.1.1.sites.stripped.vcf.gz">
32
40
  ##INFO=<ID=gnomAD_HN,Number=.,Type=String,Description="HN field from /groups/solve-rd/tmp10/projects/vip/git/vip/resources/GRCh37/gnomad.total.r2.1.1.sites.stripped.vcf.gz">
33
- ##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
34
- ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
35
- ##INFO=<ID=VIPC_S,Number=.,Type=String,Description="VIP decision tree classification (samples).">
41
+ ##INFO=<ID=phyloP,Number=.,Type=String,Description="/groups/umcg-gcc/tmp01/projects/vip/fastq/umcg-bcharbon/vip/resources/GRCh37/hg19.100way.phyloP100way.bed.gz">
36
42
  ##IncompletePenetrance=Boolean indicating if the gene is known for incomplete penetrance.
37
43
  ##InheritanceModesGene=List of inheritance modes for the gene
38
44
  ##SpliceAI_pred_DP_AG=SpliceAI predicted effect on splicing. Delta position for acceptor gain
@@ -44,7 +50,8 @@
44
50
  ##SpliceAI_pred_DS_DG=SpliceAI predicted effect on splicing. Delta score for donor gain
45
51
  ##SpliceAI_pred_DS_DL=SpliceAI predicted effect on splicing. Delta score for donor loss
46
52
  ##SpliceAI_pred_SYMBOL=SpliceAI gene symbol
47
- ##VEP="v105" time="2022-06-23 13:08:18" cache="/groups/solve-rd/tmp10/projects/vip/git/vip/resources/vep/cache/homo_sapiens_refseq/105_GRCh37" ensembl-funcgen=105.660df8f ensembl-variation=105.ac8178e ensembl=105.525fbcb ensembl-io=105.2a0a40c 1000genomes="phase3" COSMIC="92" ClinVar="202012" HGMD-PUBLIC="20204" assembly="GRCh37.p13" dbSNP="154" gencode="GENCODE 19" genebuild="2011-04" gnomAD="r2.1" polyphen="2.2.2" refseq="2020-10-26 17:03:42 - GCF_000001405.25_GRCh37.p13_genomic.gff" regbuild="1.0" sift="sift5.2.2"
53
+ ##VEP-command-line='vep --allele_number --allow_non_variant --assembly GRCh37 --buffer_size 1000 --cache --compress_output bgzip --custom [PATH]/clinvar_20230604.vcf.gz,clinVar,vcf,exact,0,CLNSIG,CLNSIGINCL,CLNREVSTAT --database 0 --dir_cache [PATH]/cache --dir_plugins [PATH]/plugins --dont_skip --exclude_predicted --fasta [PATH]/human_g1k_v37.fasta.gz --flag_pick_allele --fork 4 --format vcf --hgvs --input_file vip_normalized.vcf.gz --no_stats --numbers --offline --output_file vip_annotated.vcf.gz --plugin [PATH]/vkgl_consensus_20230401.tsv,1 --plugin AnnotSV,vip_normalized.vcf.gz.tsv,AnnotSV_ranking_score;AnnotSV_ranking_criteria;ACMG_class --polyphen s --pubmed --refseq --safe --shift_3prime --sift s --symbol --total_length --use_given_ref --vcf'
54
+ ##VEP="v109" time="2023-07-06 06:31:06" cache="/groups/umcg-gcc/tmp01/projects/vip/fastq/umcg-bcharbon/vip/resources/vep/cache/homo_sapiens_refseq/109_GRCh37" ensembl-funcgen=109.cba2db8 ensembl-variation=109.18a12b6 ensembl=109.10baaec ensembl-io=109.4946a86 1000genomes="phase3" COSMIC="92" ClinVar="202012" HGMD-PUBLIC="20204" assembly="GRCh37.p13" dbSNP="154" gencode="GENCODE 19" genebuild="2011-04" gnomADe="r2.1" polyphen="2.2.2" refseq="2020-10-26 17:03:42 - GCF_000001405.25_GRCh37.p13_genomic.gff" regbuild="1.0" sift="sift5.2.2"
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  ##VIPC=VIP decision tree classification
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  ##VIPL=VIP decision tree labels (ampersand separated)
50
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  ##VIPP=VIP decision tree path (ampersand separated)
@@ -52,6 +59,7 @@
52
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  ##VIP_Version=4.3.0
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  ##VIP_treeCommand=--input testdata_b37_chunk0_annotated.vcf.gz --config /groups/solve-rd/tmp10/projects/vip/git/vip/resources/decision_tree.json --labels 0 --path 0 --output testdata_b37_chunk0_classified.vcf.gz
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61
  ##VIP_treeVersion=3.0.0
62
+ ##VKGL=file:/groups/umcg-gcc/tmp01/projects/vip/fastq/umcg-bcharbon/vip/resources/GRCh37/vkgl_consensus_20230401.tsv'
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  ##VKGL_CL=VKGL consensus variant classification.
56
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  ##contig=<ID=1,length=249250621,assembly=b37>
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  ##contig=<ID=2,length=243199373,assembly=b37>
@@ -78,34 +86,42 @@
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  ##contig=<ID=X,length=155270560,assembly=b37>
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  ##contig=<ID=Y,length=59373566,assembly=b37>
80
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  ##contig=<ID=MT,length=16569,assembly=b37>
89
+ ##existing_InFrame_oORFs=The number of existing inFrame overlapping ORFs (inFrame oORF) at the 5 prime UTR
90
+ ##existing_OutOfFrame_oORFs=The number of existing out-of-frame overlapping ORFs (OutOfFrame oORF) at the 5 prime UTR
91
+ ##existing_uORFs=The number of existing uORFs with a stop codon within the 5 prime UTR
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  ##fileDate=20200320
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+ ##five_prime_UTR_variant_annotation=Output the annotation of a given 5 prime UTR variant
94
+ ##five_prime_UTR_variant_consequence=Output the variant consequences of a given 5 prime UTR variant: uAUG_gained, uAUG_lost, uSTOP_lost or uFrameshift
95
+ ##VIP_Version=5.6.0
96
+ ##VIP_Command=nextflow -C /groups/umcg-gcc/tmp01/projects/vip/fastq/umcg-bcharbon/vip/config/nxf_vcf.config,/groups/umcg-gcc/tmp01/projects/vip/fastq/umcg-bcharbon/vip/test/output/test_snv_proband_trio/custom.cfg -log /groups/umcg-gcc/tmp01/projects/vip/fastq/umcg-bcharbon/vip/test/output/test_snv_proband_trio/.nxf.log run /groups/umcg-gcc/tmp01/projects/vip/fastq/umcg-bcharbon/vip/vip_vcf.nf -offline -profile slurm -with-report /groups/umcg-gcc/tmp01/projects/vip/fastq/umcg-bcharbon/vip/test/output/test_snv_proband_trio/nxf_report.html -with-timeline /groups/umcg-gcc/tmp01/projects/vip/fastq/umcg-bcharbon/vip/test/output/test_snv_proband_trio/nxf_timeline.html --input /groups/umcg-gcc/tmp01/projects/vip/fastq/umcg-bcharbon/vip/test/resources/snv_proband_trio.tsv --output /groups/umcg-gcc/tmp01/projects/vip/fastq/umcg-bcharbon/vip/test/output/test_snv_proband_trio -resume
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97
  #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Patient Father MotherHasQuiteALongName Sister Nephew Unrelated
83
- 1 1701 . T C . PASS CSQ=C|intergenic_variant|MODIFIER||||||||||||||||1||||1||||||||||||||||||||||||||||||||||||||||||||P|exip_p;DP=131 GT:AD:DP:VI:VIC:VID:VIG:VIM:GQ 1|1:0,50:50:AR:.:1:64802:1:50 0|0:50,0:50:.:.:.:.:.:50 0|0:50,0:50:.:.:.:.:.:50 0|0:50,0:50:.:.:.:.:.:50 0|0:50,0:50:.:.:.:.:.:50 0|0:50,0:50:.:.:.:.:.:50
84
- 1 10042538 . C T . PASS CSQ=T|missense_variant|MODERATE|NMNAT1|64802|Transcript|NM_001297778.1|protein_coding|5/5||NM_001297778.1:c.619C>Tblablablablablabla|NP_001284707.1:p.Arg207Trp|778/3796|619/840|207/279|R/W|Cgg/Tgg|rs142968179&CM127756|1||1||1|EntrezGene|||||0.04|0.08||pathogenic||1&1|26103963&22842229&22842230|||||||0|-36|-16|17|0.00|0.00|0.00|0.00|NMNAT1|VUS|0.16572298|||AR|LP||||1:10042538-10042538|3.88948e-05|0|37133|Pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp|,T|downstream_gene_variant|MODIFIER|NMNAT1|64802|Transcript|NM_001297779.2|protein_coding||||||||||rs142968179&CM127756|1|714|1|||EntrezGene||||||||pathogenic||1&1|26103963&22842229&22842230|||||||0|-36|-16|17|0.00|0.00|0.00|0.00|NMNAT1|VUS|0.033541594|||AR|LP||||1:10042538-10042538|3.88948e-05|0|37133|Pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp|,T|missense_variant|MODERATE|NMNAT1|64802|Transcript|NM_022787.4|protein_coding|5/5||NM_022787.4:c.619C>T|NP_073624.2:p.Arg207Trp|716/3734|619/840|207/279|R/W|Cgg/Tgg|rs142968179&CM127756|1||1|||EntrezGene|||||0.04|0.08||pathogenic||1&1|26103963&22842229&22842230|||||||0|-36|-16|17|0.00|0.00|0.00|0.00|NMNAT1|VUS|0.14321531|||AR|LP||||1:10042538-10042538|3.88948e-05|0|37133|Pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp| GT:AD:DP:VI:VIC:VID:VIG:VIM:GQ 1|1:0,50:50:AR:.:1:64802:1:10 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
85
- 1 16375583 . GA G . PASS CSQ=-|intron_variant|MODIFIER|CLCNKB|1188|Transcript|NM_000085.5|protein_coding||7/19|NM_000085.5:c.656-31del|||||||rs751608665|1||1||1|EntrezGene||||||||uncertain_significance&pathogenic||1||||||||20|45|-14|-45|0.05|0.00|0.00|0.00|CLCNKB|VUS|0.032507|HP:0000951||AR|LP||||1:16375584-16375585|0.000548455|0|638508|Conflicting_interpretations_of_pathogenicity||criteria_provided&_conflicting_interpretations|LP|filter&vkgl&exit_lp|,-|frameshift_variant|HIGH|CLCNKB|1188|Transcript|NM_001165945.2|protein_coding|1/13||NM_001165945.2:c.118del|NP_001159417.2:p.Arg40GlyfsTer4|328/2174|118/1554|40/517|R/X|Agg/gg|rs751608665|1||1|||EntrezGene||||||||uncertain_significance&pathogenic||1||||||||20|45|-14|-45|0.05|0.00|0.00|0.00|CLCNKB|VUS|0.9770811|HP:0000951||AR|LP||||1:16375584-16375585|0.000548455|0|638508|Conflicting_interpretations_of_pathogenicity||criteria_provided&_conflicting_interpretations|LP|filter&vkgl&exit_lp| GT:AD:DP:VI:VIC:VID:VIG:VIM:VIS:GQ 1|0:25,25:50:AR:1_16376412_G_A,1_16376412_G_N:0:1188:1:AR_C:50 1|0:25,25:50:.:.:.:.:.:.:50 0|0:50,0:50:.:.:.:.:.:.:50 0|0:50,0:50:.:.:.:.:.:.:50 0|0:50,0:50:.:.:.:.:.:.:50 0|0:50,0:50:.:.:.:.:.:.:50
86
- 1 16376412 n_alt G N . PASS CSQ=N|splice_donor_variant|HIGH|CLCNKB|1188|Transcript|NM_000085.5|protein_coding||10/19||||||||CS1211892&CS971662|1||1||1|EntrezGene||||||||||1&1|||||||||||||||||VUS|0.373989|HP:0000951||AR||||||||||||LP|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_lp|,N|splice_donor_variant|HIGH|CLCNKB|1188|Transcript|NM_001165945.2|protein_coding||3/12||||||||CS1211892&CS971662|1||1|||EntrezGene||||||||||1&1|||||||||||||||||VUS|0.373989|HP:0000951||AR||||||||||||LP|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_lp| GT:AD:DP:VI:VIC:VID:VIG:VIM:VIS:GQ 1|0:5,45:50:AR,AD:1_16376412_G_A,1_16375583_GA_G:1:1188:1:AR_C 0|0:50,0:50:.:.:.:.:.:.: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
87
- 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|0.9855972|HP:0000951||AR|LP||||1:16376412-16376412|6.38086e-05|0|1285112|Pathogenic/Likely_pathogenic||no_assertion_criteria_provided|LP|filter&vkgl&exit_lp|,A|splice_donor_variant|HIGH|CLCNKB|1188|Transcript|NM_001165945.2|protein_coding||3/12|NM_001165945.2:c.461+1G>A|||||||rs201204502&CS1211892&CS971662|1||1|||EntrezGene||||||||||0&1&1||||||||17|-36|-28|-1|0.00|0.00|0.03|0.97|CLCNKB|VUS|0.9855972|HP:0000951||AR|LP||||1:16376412-16376412|6.38086e-05|0|1285112|Pathogenic/Likely_pathogenic||no_assertion_criteria_provided|LP|filter&vkgl&exit_lp| GT:AD:DP:VI:VIC:VID:VIG:VIM:VIS:GQ 0|1:50:50:AR:1_16375583_GA_G,1_16376412_G_N:0:1188:1:AR_C: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 0|0:50,0:50:.:.:.:.:.:.:50
88
- 1 17349219 g_ref G A . PASS CSQ=A|missense_variant|MODERATE|SDHB|6390|Transcript|NM_003000.3|protein_coding|7/8||NM_003000.3:c.649C>T|NP_002991.2:p.Arg217Cys|662/1015|649/843|217/280|R/C|Cgc/Tgc|rs200245469&CM094752&CM1210440&COSV64965760|1||-1||1|EntrezGene|||||0|1||likely_pathogenic|0&0&0&1|1&1&1&1||||||||28|6|6|5|0.00|0.00|0.00|0.00|SDHB|VUS|0.89070946|HP:0000951&HP:0003124||AD&AR|LP|||||||183735|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp| GT:AD:DP:VI:VIC:VID:VIG:VIM:GQ 1|1:0,50:50:AR:.:1:6390:1:50 1|0:45,5:50:.:.:.:.:.:50 0|0:50,0:50:.:.:.:.:.:50 1|0:25,25:50:.:.:.:.:.:50 0|0:50,0:50:.:.:.:.:.:50 0|0:50,0:50:.:.:.:.:.:50
89
- 1 17355094 . C T . PASS CSQ=T|splice_donor_variant|HIGH|SDHB|6390|Transcript|NM_003000.3|protein_coding||4/7|NM_003000.3:c.423+1G>A|||||||rs398122805&CS056774&CS062098&COSV64965540|1||-1||1|EntrezGene||||||||pathogenic|0&0&0&1|1&1&1&1|21348866&17667967&17804857&16405730&21565294&15383933|||||||-49|12|26|1|0.00|0.00|0.14|0.97|SDHB|VUS|0.9641474|HP:0003124||AD&AR|LP||||1:17355094-17355094|1.19344e-05|0|29896|Pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp| GT:AD:DP:VI:VIC:VID:VIG:VIM:GQ 1|0:5,45:50:AD:.:1:6390:1:50 0|0:50,0:50:.:.:.:.:.:50 0|0:50,0:50:.:.:.:.:.:50 0|0:50,0:50:.:.:.:.:.:50 0|0:50,0:50:.:.:.:.:.:50 0|0:50,0:50:.:.:.:.:.:50
90
- 1 152520788 symbolic1 A <DEL> . PASS CSQ=deletion|transcript_ablation|HIGH|LCE3D|84648|Transcript|NM_032563.2|protein_coding|||||||||||1||-1||1|EntrezGene|||||||||||||||||||||||||||||||||||||||||||LP|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_lp|,deletion|transcript_ablation|HIGH|LCE3E|353145|Transcript|NM_178435.4|protein_coding|||||||||||1||-1|||EntrezGene|||||||||||||||||||||||||||||||||||||||||||LP|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_lp|,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00701519957||||||||||||1||||||||||||||||||||||||||||||||||||||||||||||||VUS|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_vus|,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00905971885||||||||||||1||||||||||||||||||||||||||||||||||||||||||||||||VUS|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_vus|,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00522719201||||||||||||1||||||||||||||||||||||||||||||||||||||||||||||||VUS|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_vus|;SVLEN=-49314;SVTYPE=DEL GT:AD:DP:VI:VIC:VID:VIM:GQ 1|1:0,50:50:AR:.:1:0:50 0|0:50,0:50:.:.:.:.:50 0|0:50,0:50:.:.:.:.:50 0|0:50,0:50:.:.:.:.:50 0|0:50,0:50:.:.:.:.:50 1|0:25,25:50:.:.:.:.:50
91
- 2 321682 . T <DEL> . PASS CSQ=deletion|non_coding_transcript_exon_variant&intron_variant&feature_truncation|MODIFIER|LINC01865|105373350|Transcript|NR_146953.1|lncRNA|4/3|3/3|||685-?/2100||||||1||1||1|EntrezGene|||||||||||||||||||||||||||||||||3|1A_(+0.00)%3B3A_(1_gene%2C_+0.00)%3B5F_(+0.00)|0||||||||P|exip_p;END=321887;SVLEN=-205;SVTYPE=DEL GT:AD:DP:VI:VIC:VID:VIG:VIM:GQ 1|1:0,50:50:AR:.:1:64802:1:50 0|0:50,0:50:.:.:.:.:.:50 0|0:50,0:50:.:.:.:.:.:50 0|0:50,0:50:.:.:.:.:.:50 0|0:50,0:50:.:.:.:.:.:50 0|0:50,0:50:.:.:.:.:.:50
92
- 2 6693415 . T <DEL> . PASS CSQ=deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001914803||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524064657||||||||||||1||||1||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524052275||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524121752||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524688093||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00525576244||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524108762||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524259723||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524175972||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524198224||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524134566||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00769910345||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524344258||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524278495||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524312437||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524083163||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524770333||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00829572188||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524396085||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00909212078||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524214908||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524150456||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524239498||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524095954||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00530094654||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p,deletion|intergenic_variant|MODIFIER||||||||||||||||1||||||||||||||||||||||||||||||||||||||3|1B_(-0.60)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6||||||||P|exip_p|;END=6707844;SVLEN=-14429;SVTYPE=DEL GT:AD:DP:VI:VIC:VID:VIG:VIM:GQ 1|1:0,50:50:AR:.:1:64802:1:50 0|0:50,0:50:.:.:.:.:.:50 0|0:50,0:50:.:.:.:.:.:50 0|0:50,0:50:.:.:.:.:.:50 0|0:50,0:50:.:.:.:.:.:50 0|0:50,0:50:.:.:.:.:.:50
93
- 4 106320294 . G A . PASS CSQ=A|missense_variant|MODERATE|PPA2|27068|Transcript|NM_006903.4|protein_coding|7/11||NM_006903.4:c.596C>T|NP_008834.3:p.Pro199Leu|616/1586|596/918|199/305|P/L|cCg/cTg|rs138215926&CM1610192&COSV58994362|1||-1|||EntrezGene|||||0|0.985||pathogenic|0&0&1|1&1&1|27523597|||||||-34|27|-2|-43|0.00|0.00|0.00|0.00|PPA2|VUS|0.8097311|||AR|LP||||4:106320294-106320294|0.000211803|0|372226|Likely_pathogenic||criteria_provided&_single_submitter|LP|filter&vkgl&exit_lp|,A|missense_variant|MODERATE|PPA2|27068|Transcript|NM_176866.2|protein_coding|4/8||NM_176866.2:c.377C>T|NP_789842.2:p.Pro126Leu|397/1367|377/699|126/232|P/L|cCg/cTg|rs138215926&CM1610192&COSV58994362|1||-1|||EntrezGene|||||0|0.992||pathogenic|0&0&1|1&1&1|27523597|||||||-34|27|-2|-43|0.00|0.00|0.00|0.00|PPA2|VUS|0.7550335|||AR|LP||||4:106320294-106320294|0.000211803|0|372226|Likely_pathogenic||criteria_provided&_single_submitter|LP|filter&vkgl&exit_lp|,A|missense_variant|MODERATE|PPA2|27068|Transcript|NM_176867.3|protein_coding|2/6||NM_176867.3:c.185C>T|NP_789843.2:p.Pro62Leu|205/1175|185/507|62/168|P/L|cCg/cTg|rs138215926&CM1610192&COSV58994362|1||-1|||EntrezGene|||||0|0.995||pathogenic|0&0&1|1&1&1|27523597|||||||-34|27|-2|-43|0.00|0.00|0.00|0.00|PPA2|VUS|0.8145551|||AR|LP||||4:106320294-106320294|0.000211803|0|372226|Likely_pathogenic||criteria_provided&_single_submitter|LP|filter&vkgl&exit_lp|,A|missense_variant|MODERATE|PPA2|27068|Transcript|NM_176869.3|protein_coding|8/12||NM_176869.3:c.683C>T|NP_789845.1:p.Pro228Leu|695/1665|683/1005|228/334|P/L|cCg/cTg|rs138215926&CM1610192&COSV58994362|1||-1||1|EntrezGene|||||0|0.993||pathogenic|0&0&1|1&1&1|27523597|||||||-34|27|-2|-43|0.00|0.00|0.00|0.00|PPA2|VUS|0.76490384|||AR|LP||||4:106320294-106320294|0.000211803|0|372226|Likely_pathogenic||criteria_provided&_single_submitter|LP|filter&vkgl&exit_lp|,A|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001994744|promoter_flanking_region||||||||||rs138215926&CM1610192&COSV58994362|1|||||||||||||pathogenic|0&0&1|1&1&1|27523597|||||||||||||||||||||||||4:106320294-106320294|0.000211803|0|372226|Likely_pathogenic||criteria_provided&_single_submitter|LP|filter&vkgl&clinVar&exit_lp| GT:AD:DP:VI:VIC:VID:VIG:VIM:GQ 1|1:0,50:50:AR:.:1:27068:1:50 1|0:25,25:50:.:.:.:.:.:50 0|0:50,0:50:.:.:.:.:.:50 0|0:50,0:50:.:.:.:.:.:50 0|0:50,0:50:.:.:.:.:.:50 1|1:0,50:50:.:.:.:.:.:50
94
- 9 107546633 . AAAGAT A . PASS CSQ=-|frameshift_variant|HIGH|ABCA1|19|Transcript|NM_005502.4|protein_coding|50/50||NM_005502.4:c.6744_6748del|NP_005493.2:p.Phe2250ThrfsTer3|7057-7061/10408|6744-6748/6786|2248-2250/2261|TSF/TX|acATCTTtt/actt||1||-1||1|EntrezGene|||||||||||||||||||||||||||VUS|0.9823047|HP:0000951||AD&AR||||||||||||LP|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_lp| GT:AD:DP:VI:VIC:VID:VIG:VIM:GQ 1|1:0,10:10:AR:.:0:19:1 0|1:1,49:50:.:.:.:.:.:50 1|0:0,50:50:.:.:.:.:.:50 0|0:50,0:50:.:.:.:.:.:50 0|0:50,0:50:.:.:.:.:.:50 0|0:50,0:50:.:.:.:.:.:50
95
- 9 107584864 . AC A . PASS CSQ=-|frameshift_variant|HIGH|ABCA1|19|Transcript|NM_005502.4|protein_coding|19/50||NM_005502.4:c.2740del|NP_005493.2:p.Val914TrpfsTer8|3053/10408|2740/6786|914/2261|V/X|Gtg/tg||1||-1||1|EntrezGene||||||||||||||||||33|-42|28|1|0.00|0.00|0.10|0.00|ABCA1|VUS|0.98804027|HP:0000951||AD&AR|LP|||||||||||LP|filter&vkgl&exit_lp| GT:AD:DP:VI:VIC:VID:VIG:VIM:GQ 1|0:10,90:50:AD:.:1:19:1:50 0|0:50,0:50:.:.:.:.:.:50 0|0:50,0:50:.:.:.:.:.:50 0|0:50,0:50:.:.:.:.:.:50 0|0:50,0:50:.:.:.:.:.:50 0|0:50,0:50:.:.:.:.:.:50
96
- 10 126091499 . G C . PASS CSQ=C|stop_gained|HIGH|OAT|4942|Transcript|NM_000274.4|protein_coding|7/10||NM_000274.4:c.897C>G|NP_000265.1:p.Tyr299Ter|977/2039|897/1320|299/439|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808|||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.979408|||AR|LP||||10:126091499-126091499|1.59133e-05|0|176|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp|,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001171814.2|protein_coding|6/9||NM_001171814.2:c.483C>G|NP_001165285.1:p.Tyr161Ter|749/1811|483/906|161/301|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808|||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.97846687|||AR|LP||||10:126091499-126091499|1.59133e-05|0|176|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp|,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322965.2|protein_coding|7/10||NM_001322965.2:c.897C>G|NP_001309894.1:p.Tyr299Ter|972/2034|897/1320|299/439|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808|||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.979408|||AR|LP||||10:126091499-126091499|1.59133e-05|0|176|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp|,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322966.2|protein_coding|8/11||NM_001322966.2:c.897C>G|NP_001309895.1:p.Tyr299Ter|1292/2354|897/1320|299/439|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1||1|EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808|||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.9796912|||AR|LP||||10:126091499-126091499|1.59133e-05|0|176|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp|,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322967.2|protein_coding|8/11||NM_001322967.2:c.897C>G|NP_001309896.1:p.Tyr299Ter|1097/2159|897/1320|299/439|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808|||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.9819772|||AR|LP||||10:126091499-126091499|1.59133e-05|0|176|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp|,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322968.2|protein_coding|9/12||NM_001322968.2:c.897C>G|NP_001309897.1:p.Tyr299Ter|1184/2246|897/1320|299/439|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808|||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.9819772|||AR|LP||||10:126091499-126091499|1.59133e-05|0|176|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp|,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322969.2|protein_coding|8/11||NM_001322969.2:c.897C>G|NP_001309898.1:p.Tyr299Ter|1064/2126|897/1320|299/439|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808|||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.9819772|||AR|LP||||10:126091499-126091499|1.59133e-05|0|176|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp|,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322970.2|protein_coding|9/12||NM_001322970.2:c.897C>G|NP_001309899.1:p.Tyr299Ter|1280/2342|897/1320|299/439|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808|||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.9796912|||AR|LP||||10:126091499-126091499|1.59133e-05|0|176|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp|,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322971.2|protein_coding|5/8||NM_001322971.2:c.576C>G|NP_001309900.1:p.Tyr192Ter|656/1718|576/999|192/332|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808|||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.9760591|||AR|LP||||10:126091499-126091499|1.59133e-05|0|176|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp|,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322974.2|protein_coding|7/10||NM_001322974.2:c.297C>G|NP_001309903.1:p.Tyr99Ter|863/1925|297/720|99/239|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808|||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.9775237|||AR|LP||||10:126091499-126091499|1.59133e-05|0|176|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp| GT:AD:DP:VI:VIC:VID:VIG:VIM:GQ 1|1:0,50:50:AR:.:1:4942:1:50 1|0:25,25:50:.:.:.:.:.:50 0|0:50,0:50:.:.:.:.:.:50 0|0:50,0:50:.:.:.:.:.:50 0|0:50,0:50:.:.:.:.:.:50 0|0:50,0:50:.:.:.:.:.:50
97
- 13 77570128 . G A . PASS CSQ=A|missense_variant|MODERATE|CLN5|1203|Transcript|NM_001366624.2|protein_coding|3/5||NM_001366624.2:c.431G>A|NP_001353553.1:p.Cys144Tyr|449/5286|431/594|144/197|C/Y|tGt/tAt|rs1566219136|1||1|||EntrezGene|||||0|0.995||pathogenic||1||||||||-27|-43|-27|-1|0.00|0.00|0.01|0.00|CLN5|VUS|0.79378206|||AR|LP|||||||623394|Pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp|,A|missense_variant|MODERATE|CLN5|1203|Transcript|NM_006493.4|protein_coding|3/4||NM_006493.4:c.431G>A|NP_006484.2:p.Cys144Tyr|449/5243|431/1077|144/358|C/Y|tGt/tAt|rs1566219136|1||1||1|EntrezGene|||||0|0.999||pathogenic||1||||||||-27|-43|-27|-1|0.00|0.00|0.01|0.00|CLN5|VUS|0.862269|||AR|LP|||||||623394|Pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp| GT:AD:DP:VIC:VID:VIM:GQ 1|1:0,50:50:.:1:0:50 1|1:0,50:50:.:.:.:50 0|0:50,0:50:.:.:.:50 0|0:50,0:50:.:.:.:50 0|0:50,0:50:.:.:.:50 0|0:50,0:50:.:.:.:50
98
- 14 89307838 . C T . PASS CSQ=T|stop_gained|HIGH|TTC8|123016|Transcript|NM_001288781.1|protein_coding|6/16||NM_001288781.1:c.529C>T|NP_001275710.1:p.Gln177Ter|725/2378|529/1596|177/531|Q/*|Cag/Tag|rs376035653|1||1||1|EntrezGene||||||||||||||||||3|-22|-8|20|0.00|0.00|0.00|0.05|TTC8|VUS|0.9807194|HP:0000951||AR|LP||||14:89307838-89307838|3.99307e-06|0|997900|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp|,T|5_prime_UTR_variant|MODIFIER|TTC8|123016|Transcript|NM_001288782.1|protein_coding|6/14||NM_001288782.1:c.-34C>T||725/2298|||||rs376035653|1||1|||EntrezGene||||||||||||||||||3|-22|-8|20|0.00|0.00|0.00|0.05|TTC8|VUS|0.009629895|HP:0000951||AR|LP||||14:89307838-89307838|3.99307e-06|0|997900|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp|,T|intron_variant|MODIFIER|TTC8|123016|Transcript|NM_001288783.1|protein_coding||5/14|NM_001288783.1:c.-199+298C>T|||||||rs376035653|1||1|||EntrezGene||||||||||||||||||3|-22|-8|20|0.00|0.00|0.00|0.05|TTC8|VUS|0.0075686513|HP:0000951||AR|LP||||14:89307838-89307838|3.99307e-06|0|997900|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp|,T|stop_gained|HIGH|TTC8|123016|Transcript|NM_001366535.2|protein_coding|5/13||NM_001366535.2:c.529C>T|NP_001353464.1:p.Gln177Ter|586/5160|529/1434|177/477|Q/*|Cag/Tag|rs376035653|1||1|||EntrezGene||||||||||||||||||3|-22|-8|20|0.00|0.00|0.00|0.05|TTC8|VUS|0.9817811|HP:0000951||AR|LP||||14:89307838-89307838|3.99307e-06|0|997900|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp|,T|intron_variant|MODIFIER|TTC8|123016|Transcript|NM_001366536.2|protein_coding||4/11|NM_001366536.2:c.459+298C>T|||||||rs376035653|1||1|||EntrezGene||||||||||||||||||3|-22|-8|20|0.00|0.00|0.00|0.05|TTC8|VUS|0.0075686513|HP:0000951||AR|LP||||14:89307838-89307838|3.99307e-06|0|997900|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp|,T|stop_gained|HIGH|TTC8|123016|Transcript|NM_144596.4|protein_coding|6/15||NM_144596.4:c.559C>T|NP_653197.2:p.Gln187Ter|616/2183|559/1548|187/515|Q/*|Cag/Tag|rs376035653|1||1|||EntrezGene||||||||||||||||||3|-22|-8|20|0.00|0.00|0.00|0.05|TTC8|VUS|0.98182434|HP:0000951||AR|LP||||14:89307838-89307838|3.99307e-06|0|997900|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp|,T|stop_gained|HIGH|TTC8|123016|Transcript|NM_198309.3|protein_coding|6/15||NM_198309.3:c.529C>T|NP_938051.1:p.Gln177Ter|725/2300|529/1518|177/505|Q/*|Cag/Tag|rs376035653|1||1|||EntrezGene||||||||||||||||||3|-22|-8|20|0.00|0.00|0.00|0.05|TTC8|VUS|0.9807194|HP:0000951||AR|LP||||14:89307838-89307838|3.99307e-06|0|997900|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp|,T|intron_variant|MODIFIER|TTC8|123016|Transcript|NM_198310.3|protein_coding||5/13|NM_198310.3:c.459+298C>T|||||||rs376035653|1||1|||EntrezGene||||||||||||||||||3|-22|-8|20|0.00|0.00|0.00|0.05|TTC8|VUS|0.0075686513|HP:0000951||AR|LP||||14:89307838-89307838|3.99307e-06|0|997900|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp|,T|non_coding_transcript_exon_variant|MODIFIER|TTC8|123016|Transcript|NR_159362.2|misc_RNA|5/15||NR_159362.2:n.586C>T||586/5304|||||rs376035653|1||1|||EntrezGene||||||||||||||||||3|-22|-8|20|0.00|0.00|0.00|0.05|TTC8|VUS|0.08789039|HP:0000951||AR|LP||||14:89307838-89307838|3.99307e-06|0|997900|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp| GT:AD:DP:VI:VIC:VID:VIM:GQ 1|0:25,25:50:AD:.:1:0:50 0|0:50,0:50:.:.:.:.:50 0|0:50,0:50:.:.:.:.:50 0|0:50,0:50:.:.:.:.:50 0|0:50,0:50:.:.:.:.:50 0|0:50,0:50:.:.:.:.:50
99
- 14 89310195 . G A . PASS CSQ=A|splice_donor_variant|HIGH|TTC8|123016|Transcript|NM_001288781.1|protein_coding||7/15|NM_001288781.1:c.594+1G>A|||||||rs587777808&CD056477&CS056440|1||1||1|EntrezGene||||||||pathogenic||1&1&1|16308660|||||||32|-45|32|-1|0.00|0.00|0.00|1.00|TTC8|VUS|0.9949398|HP:0000951||AR|LP|||||||2531|Pathogenic||no_assertion_criteria_provided|LP|filter&vkgl&exit_lp|,A|intron_variant|MODIFIER|TTC8|123016|Transcript|NM_001288782.1|protein_coding||6/13|NM_001288782.1:c.30+2294G>A|||||||rs587777808&CD056477&CS056440|1||1|||EntrezGene||||||||pathogenic||1&1&1|16308660|||||||32|-45|32|-1|0.00|0.00|0.00|1.00|TTC8|VUS|0.19432564|HP:0000951||AR|LP|||||||2531|Pathogenic||no_assertion_criteria_provided|LP|filter&vkgl&exit_lp|,A|splice_donor_variant|HIGH|TTC8|123016|Transcript|NM_001288783.1|protein_coding||6/14|NM_001288783.1:c.-154+1G>A|||||||rs587777808&CD056477&CS056440|1||1|||EntrezGene||||||||pathogenic||1&1&1|16308660|||||||32|-45|32|-1|0.00|0.00|0.00|1.00|TTC8|VUS|0.9949398|HP:0000951||AR|LP|||||||2531|Pathogenic||no_assertion_criteria_provided|LP|filter&vkgl&exit_lp|,A|splice_donor_variant|HIGH|TTC8|123016|Transcript|NM_001366535.2|protein_coding||6/12|NM_001366535.2:c.594+1G>A|||||||rs587777808&CD056477&CS056440|1||1|||EntrezGene||||||||pathogenic||1&1&1|16308660|||||||32|-45|32|-1|0.00|0.00|0.00|1.00|TTC8|VUS|0.9949398|HP:0000951||AR|LP|||||||2531|Pathogenic||no_assertion_criteria_provided|LP|filter&vkgl&exit_lp|,A|splice_donor_variant|HIGH|TTC8|123016|Transcript|NM_001366536.2|protein_coding||5/11|NM_001366536.2:c.504+1G>A|||||||rs587777808&CD056477&CS056440|1||1|||EntrezGene||||||||pathogenic||1&1&1|16308660|||||||32|-45|32|-1|0.00|0.00|0.00|1.00|TTC8|VUS|0.9949398|HP:0000951||AR|LP|||||||2531|Pathogenic||no_assertion_criteria_provided|LP|filter&vkgl&exit_lp|,A|splice_donor_variant|HIGH|TTC8|123016|Transcript|NM_144596.4|protein_coding||7/14|NM_144596.4:c.624+1G>A|||||||rs587777808&CD056477&CS056440|1||1|||EntrezGene||||||||pathogenic||1&1&1|16308660|||||||32|-45|32|-1|0.00|0.00|0.00|1.00|TTC8|VUS|0.9949398|HP:0000951||AR|LP|||||||2531|Pathogenic||no_assertion_criteria_provided|LP|filter&vkgl&exit_lp|,A|splice_donor_variant|HIGH|TTC8|123016|Transcript|NM_198309.3|protein_coding||7/14|NM_198309.3:c.594+1G>A|||||||rs587777808&CD056477&CS056440|1||1|||EntrezGene||||||||pathogenic||1&1&1|16308660|||||||32|-45|32|-1|0.00|0.00|0.00|1.00|TTC8|VUS|0.9949398|HP:0000951||AR|LP|||||||2531|Pathogenic||no_assertion_criteria_provided|LP|filter&vkgl&exit_lp|,A|splice_donor_variant|HIGH|TTC8|123016|Transcript|NM_198310.3|protein_coding||6/13|NM_198310.3:c.504+1G>A|||||||rs587777808&CD056477&CS056440|1||1|||EntrezGene||||||||pathogenic||1&1&1|16308660|||||||32|-45|32|-1|0.00|0.00|0.00|1.00|TTC8|VUS|0.9949398|HP:0000951||AR|LP|||||||2531|Pathogenic||no_assertion_criteria_provided|LP|filter&vkgl&exit_lp|,A|splice_donor_variant&non_coding_transcript_variant|HIGH|TTC8|123016|Transcript|NR_159362.2|misc_RNA||6/14|NR_159362.2:n.651+1G>A|||||||rs587777808&CD056477&CS056440|1||1|||EntrezGene||||||||pathogenic||1&1&1|16308660|||||||32|-45|32|-1|0.00|0.00|0.00|1.00|TTC8|VUS|0.9951024|HP:0000951||AR|LP|||||||2531|Pathogenic||no_assertion_criteria_provided|LP|filter&vkgl&exit_lp| GT:AD:DP:VI:VIC:VID:VIG:GQ 1|1:0,9:9:AR:.:0:123016:50 0|1:.:10:.:.:.:.:50 0|1:50:50:.:.:.:.:50 0|0:50,0:50:.:.:.:.:50 0|0:50,0:50:.:.:.:.:50 0|0:50,0:50:.:.:.:.:50
100
- 14 89336407 . TG T . PASS CSQ=-|frameshift_variant|HIGH|TTC8|123016|Transcript|NM_001288781.1|protein_coding|12/16||NM_001288781.1:c.963del|NP_001275710.1:p.Met321IlefsTer15|1159/2378|963/1596|321/531|M/X|atG/at|rs1431207606|1||1||1|EntrezGene||||||||||||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.9807489|HP:0000951||AR|LP||||14:89336408-89336409|1.19537e-05|0|930561|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp|,-|frameshift_variant|HIGH|TTC8|123016|Transcript|NM_001288782.1|protein_coding|10/14||NM_001288782.1:c.321del|NP_001275711.1:p.Met107IlefsTer15|1079/2298|321/954|107/317|M/X|atG/at|rs1431207606|1||1|||EntrezGene||||||||||||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.9838007|HP:0000951||AR|LP||||14:89336408-89336409|1.19537e-05|0|930561|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp|,-|frameshift_variant|HIGH|TTC8|123016|Transcript|NM_001288783.1|protein_coding|11/15||NM_001288783.1:c.198del|NP_001275712.1:p.Met66IlefsTer15|1051/2270|198/831|66/276|M/X|atG/at|rs1431207606|1||1|||EntrezGene||||||||||||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.98078203|HP:0000951||AR|LP||||14:89336408-89336409|1.19537e-05|0|930561|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp|,-|frameshift_variant|HIGH|TTC8|123016|Transcript|NM_001366535.2|protein_coding|10/13||NM_001366535.2:c.885del|NP_001353464.1:p.Met295IlefsTer15|942/5160|885/1434|295/477|M/X|atG/at|rs1431207606|1||1|||EntrezGene||||||||||||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.9797095|HP:0000951||AR|LP||||14:89336408-89336409|1.19537e-05|0|930561|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp|,-|frameshift_variant|HIGH|TTC8|123016|Transcript|NM_001366536.2|protein_coding|9/12||NM_001366536.2:c.795del|NP_001353465.1:p.Met265IlefsTer15|852/5070|795/1344|265/447|M/X|atG/at|rs1431207606|1||1|||EntrezGene||||||||||||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.9856574|HP:0000951||AR|LP||||14:89336408-89336409|1.19537e-05|0|930561|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp|,-|frameshift_variant|HIGH|TTC8|123016|Transcript|NM_144596.4|protein_coding|11/15||NM_144596.4:c.915del|NP_653197.2:p.Met305IlefsTer15|972/2183|915/1548|305/515|M/X|atG/at|rs1431207606|1||1|||EntrezGene||||||||||||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.9619866|HP:0000951||AR|LP||||14:89336408-89336409|1.19537e-05|0|930561|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp|,-|frameshift_variant|HIGH|TTC8|123016|Transcript|NM_198309.3|protein_coding|11/15||NM_198309.3:c.885del|NP_938051.1:p.Met295IlefsTer15|1081/2300|885/1518|295/505|M/X|atG/at|rs1431207606|1||1|||EntrezGene||||||||||||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.9801349|HP:0000951||AR|LP||||14:89336408-89336409|1.19537e-05|0|930561|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp|,-|frameshift_variant|HIGH|TTC8|123016|Transcript|NM_198310.3|protein_coding|10/14||NM_198310.3:c.795del|NP_938052.1:p.Met265IlefsTer15|991/2210|795/1428|265/475|M/X|atG/at|rs1431207606|1||1|||EntrezGene||||||||||||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.9853147|HP:0000951||AR|LP||||14:89336408-89336409|1.19537e-05|0|930561|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp|,-|non_coding_transcript_exon_variant|MODIFIER|TTC8|123016|Transcript|NR_159362.2|misc_RNA|11/15||NR_159362.2:n.1002del||1002/5304|||||rs1431207606|1||1|||EntrezGene||||||||||||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.10411882|HP:0000951||AR|LP||||14:89336408-89336409|1.19537e-05|0|930561|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp| GT:AD:DP:VI:VIC:VID:VIG:VIM:GQ 1|1:0,50:50:.:.:.:.:.:50 1|0:25,25:50:.:.:.:.:.:50 0|0:50,0:50:.:.:.:.:.:50 0|0:50,0:50:.:.:.:.:.:50 0|0:50,0:50:.:.:.:.:.:50 0|0:50,0:50:.:.:.:.:.:50
101
- 14 105167860 . T G . PASS CSQ=G|missense_variant|MODERATE|INF2|64423|Transcript|NM_001031714.4|protein_coding|2/22||NM_001031714.4:c.158T>G|NP_001026884.3:p.Leu53Arg|289/7566|158/3723|53/1240|L/R|cTg/cGg||1||1|||EntrezGene|||||0|0.999||||||||||||-28|-2|37|-2|0.00|0.00|0.00|0.00|INF2|VUS|0.9012849|||AD|LP|||||||||||LP|filter&vkgl&exit_lp|,G|missense_variant|MODERATE|INF2|64423|Transcript|NM_022489.4|protein_coding|2/23||NM_022489.4:c.158T>G|NP_071934.3:p.Leu53Arg|289/7623|158/3750|53/1249|L/R|cTg/cGg||1||1||1|EntrezGene|||||0|0.999||||||||||||-28|-2|37|-2|0.00|0.00|0.00|0.00|INF2|VUS|0.9012849|||AD|LP|||||||||||LP|filter&vkgl&exit_lp|,G|missense_variant|MODERATE|INF2|64423|Transcript|NM_032714.3|protein_coding|2/5||NM_032714.3:c.158T>G|NP_116103.1:p.Leu53Arg|289/1692|158/705|53/234|L/R|cTg/cGg||1||1|||EntrezGene|||||0|0.999||||||||||||-28|-2|37|-2|0.00|0.00|0.00|0.00|INF2|VUS|0.9012849|||AD|LP|||||||||||LP|filter&vkgl&exit_lp| GT:AD:DP:VI:VIC:VID:VIM:GQ 1|1:0,50:50:AR:.:1:0:50 0|0:50,0:50:.:.:.:.:50 1|0:45,5:50:.:.:.:.:50 0|0:50,0:50:.:.:.:.:50 1|0:25,25:50:.:.:.:.:50 0|0:50,0:50:.:.:.:.:50
102
- 17 29556064 . AC A . PASS CSQ=-|frameshift_variant|HIGH|NF1|4763|Transcript|NM_000267.3|protein_coding|21/57||NM_000267.3:c.2433del|NP_000258.1:p.Ile812LeufsTer9|2816/12362|2433/8457|811/2818|T/X|acC/ac||1||1|||EntrezGene|||||||1|||||||||||-22|-11|12|25|0.00|0.00|0.00|0.00|NF1|VUS|0.9913782|HP:0000951|1|AD|LP|||||||||||LP|filter&vkgl&exit_lp|,-|frameshift_variant|HIGH|NF1|4763|Transcript|NM_001042492.3|protein_coding|21/58||NM_001042492.3:c.2433del|NP_001035957.1:p.Ile812LeufsTer9|2766/12373|2433/8520|811/2839|T/X|acC/ac||1||1||1|EntrezGene|||||||1|||||||||||-22|-11|12|25|0.00|0.00|0.00|0.00|NF1|VUS|0.9913782|HP:0000951|1|AD|LP|||||||||||LP|filter&vkgl&exit_lp| GT:AD:DP:VIC:VID:VIM:GQ 1|1:0,50:50:.:1:0:50 1|1:0,50:50:.:.:.:50 0|0:50,0:50:.:.:.:50 1|0:25,25:50:.:.:.:50 0|0:50,0:50:.:.:.:50 1|0:25,25:50:.:.:.:50
103
- 17 29585422 . A G . PASS CSQ=G|missense_variant|MODERATE|NF1|4763|Transcript|NM_000267.3|protein_coding|31/57||NM_000267.3:c.4171A>G|NP_000258.1:p.Arg1391Gly|4554/12362|4171/8457|1391/2818|R/G|Aga/Gga|rs1555618515&CM1211610|1||1|||EntrezGene|||||0|0.962||pathogenic||1&1||||||||-48|2|28|-27|0.00|0.00|0.01|0.00|NF1|VUS|0.6458939|HP:0000951|1|AD|LP|||||||457686|Pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp|,G|missense_variant|MODERATE|NF1|4763|Transcript|NM_001042492.3|protein_coding|32/58||NM_001042492.3:c.4234A>G|NP_001035957.1:p.Arg1412Gly|4567/12373|4234/8520|1412/2839|R/G|Aga/Gga|rs1555618515&CM1211610|1||1||1|EntrezGene|||||0|0.988||pathogenic||1&1||||||||-48|2|28|-27|0.00|0.00|0.01|0.00|NF1|VUS|0.7539552|HP:0000951|1|AD|LP|||||||457686|Pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|filter&vkgl&exit_lp| GT:AD:DP:VI:VIC:VID:VIM:GQ 1|1:0,50:50:AR:.:1:0 0|1:.:10:.:.:.:.:50 0|0:50,0:50:.:.:.:.:50 0|0:50,0:50:.:.:.:.:50 0|0:50,0:50:.:.:.:.:50 0|0:50,0:50:.:.:.:.:50
104
- 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||||||||-42|41|-34|8|0.00|0.00|0.00|0.00|NF1|VUS|0.8564539|HP:0000951|1|AD|LP|||||||996527|Likely_pathogenic||criteria_provided&_single_submitter|LP|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||||||||-42|41|-34|8|0.00|0.00|0.00|0.00|NF1|VUS|0.8564539|HP:0000951|1|AD|LP|||||||996527|Likely_pathogenic||criteria_provided&_single_submitter|LP|filter&vkgl&exit_lp| GT:AD:DP:VI:VIC:VID:VIG:VIM:VIS:GQ 1|0:25,25:50:AR,AD:17_29683983_C_T:0:4763:1:AD_IP,AR_C: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 0|0:50,0:50:.:.:.:.:.:.:50
105
- 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|0.99177766|HP:0000951|1|AD|LP|||||||||||LP|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|0.9919058|HP:0000951|1|AD|LP|||||||||||LP|filter&vkgl&exit_lp| GT:AD:DP:VI:VIC:VID:VIG:VIM:VIS:GQ .|.:25,25:50:AR,AD:17_29663879_T_G:1:4763:1:AR_C:50 0|0:50,0:50:.:.:.:.:.:.:50 0|0:50,0:50:.:.:.:.:.:.:50 0|0:50,0:50:.:.:.:.:.:.:50 0|0:50,0:50:.:.:.:.:.:.:50 0|0:50,0:50:.:.:.:.:.:.:50
106
- 19 11224051 . C CGTGGTCGCTCTGGACACGGAG . PASS CSQ=TCGCTCTGGACACGGAGGTGG|inframe_insertion|MODERATE|LDLR|3949|Transcript|NM_000527.5|protein_coding|9/18||NM_000527.5:c.1289_1309dup|NP_000518.1:p.Val430_Val436dup|1395-1396/5173|1309-1310/2583|437/860|A/VALDTEVA|gcc/gTCGCTCTGGACACGGAGGTGGcc||1||1||1|EntrezGene|||||||25||||||||||||||||||||VUS|0.27201134|HP:0000951&HP:0003124||AD&AR|LP|||||||||||LP|filter&vkgl&exit_lp|,TCGCTCTGGACACGGAGGTGG|inframe_insertion|MODERATE|LDLR|3949|Transcript|NM_001195798.2|protein_coding|9/18||NM_001195798.2:c.1289_1309dup|NP_001182727.1:p.Val430_Val436dup|1395-1396/5167|1309-1310/2577|437/858|A/VALDTEVA|gcc/gTCGCTCTGGACACGGAGGTGGcc||1||1|||EntrezGene|||||||25||||||||||||||||||||VUS|0.27201134|HP:0000951&HP:0003124||AD&AR|LP|||||||||||LP|filter&vkgl&exit_lp|,TCGCTCTGGACACGGAGGTGG|inframe_insertion|MODERATE|LDLR|3949|Transcript|NM_001195799.2|protein_coding|8/17||NM_001195799.2:c.1166_1186dup|NP_001182728.1:p.Val389_Val395dup|1272-1273/5050|1186-1187/2460|396/819|A/VALDTEVA|gcc/gTCGCTCTGGACACGGAGGTGGcc||1||1|||EntrezGene|||||||25||||||||||||||||||||VUS|0.26963568|HP:0000951&HP:0003124||AD&AR|LP|||||||||||LP|filter&vkgl&exit_lp|,TCGCTCTGGACACGGAGGTGG|inframe_insertion|MODERATE|LDLR|3949|Transcript|NM_001195800.2|protein_coding|7/16||NM_001195800.2:c.785_805dup|NP_001182729.1:p.Val262_Val268dup|891-892/4669|805-806/2079|269/692|A/VALDTEVA|gcc/gTCGCTCTGGACACGGAGGTGGcc||1||1|||EntrezGene|||||||25||||||||||||||||||||VUS|0.3952981|HP:0000951&HP:0003124||AD&AR|LP|||||||||||LP|filter&vkgl&exit_lp|,TCGCTCTGGACACGGAGGTGG|inframe_insertion|MODERATE|LDLR|3949|Transcript|NM_001195803.2|protein_coding|8/16||NM_001195803.2:c.908_928dup|NP_001182732.1:p.Val303_Val309dup|1014-1015/4639|928-929/2049|310/682|A/VALDTEVA|gcc/gTCGCTCTGGACACGGAGGTGGcc||1||1|||EntrezGene|||||||25||||||||||||||||||||VUS|0.30903387|HP:0000951&HP:0003124||AD&AR|LP|||||||||||LP|filter&vkgl&exit_lp| GT:AD:DP:VI:VIC:VID:VIG:VIM:GQ 1|1:.:10:AR:.:0:3949:1:50 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
107
- 19 17449399 . C T . PASS . GT:AD:DP:VI:VIC:VID:VIM:GQ 1|0:25,25:50:AD:.:1:0:50 0|0:50,0:50:.:.:.:.:50 0|0:50,0:50:.:.:.:.:50 0|0:50,0:50:.:.:.:.:50 0|0:50,0:50:.:.:.:.:50 0|0:50,0:50:.:.:.:.:50
108
- 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|0.9804278|HP:0000951||AR|LP|||||||||||LP|filter&vkgl&exit_lp|,-|frameshift_variant|HIGH|GTPBP3|84705|Transcript|NM_001195422.1|protein_coding|8/9||NM_001195422.1:c.1187del|NP_001182351.1:p.Asn396ThrfsTer26|1209/2595|1187/1545|396/514|N/X|aAc/ac||1||1|||EntrezGene|||||||1|||||||||||34|33|-7|33|0.01|0.00|0.00|0.00|GTPBP3|VUS|0.98119754|HP:0000951||AR|LP|||||||||||LP|filter&vkgl&exit_lp|,-|frameshift_variant|HIGH|GTPBP3|84705|Transcript|NM_032620.4|protein_coding|8/9||NM_032620.4:c.1121del|NP_116009.2:p.Asn374ThrfsTer26|1180/2566|1121/1479|374/492|N/X|aAc/ac||1||1|||EntrezGene|||||||1|||||||||||34|33|-7|33|0.01|0.00|0.00|0.00|GTPBP3|VUS|0.98185974|HP:0000951||AR|LP|||||||||||LP|filter&vkgl&exit_lp|,-|frameshift_variant|HIGH|GTPBP3|84705|Transcript|NM_133644.4|protein_coding|7/8||NM_133644.4:c.1217del|NP_598399.2:p.Asn406ThrfsTer26|1276/2662|1217/1575|406/524|N/X|aAc/ac||1||1||1|EntrezGene|||||||1|||||||||||34|33|-7|33|0.01|0.00|0.00|0.00|GTPBP3|VUS|0.97986597|HP:0000951||AR|LP|||||||||||LP|filter&vkgl&exit_lp| GT:AD:DP:VIC:VID:VIM:GQ 1|1:0,50:50:.:1:0:50 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
109
- 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||||||||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.14842245||||||||22:50721546-50721546|4.49665e-06|0|||||VUS|filter&vkgl&clinVar&gnomad&effect&sift&polyphen&impact&exit_vus|,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||||||||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.14842245||||||||22:50721546-50721546|4.49665e-06|0|||||VUS|filter&vkgl&clinVar&gnomad&effect&sift&polyphen&impact&exit_vus|,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||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.92206705||||||||22:50721546-50721546|4.49665e-06|0|||||LP|filter&vkgl&clinVar&gnomad&effect&sift&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||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.92206705||||||||22:50721546-50721546|4.49665e-06|0|||||LP|filter&vkgl&clinVar&gnomad&effect&sift&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||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.92206705||||||||22:50721546-50721546|4.49665e-06|0|||||LP|filter&vkgl&clinVar&gnomad&effect&sift&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||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.92206705||||||||22:50721546-50721546|4.49665e-06|0|||||LP|filter&vkgl&clinVar&gnomad&effect&sift&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||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.92206705||||||||22:50721546-50721546|4.49665e-06|0|||||LP|filter&vkgl&clinVar&gnomad&effect&sift&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||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.92206705||||||||22:50721546-50721546|4.49665e-06|0|||||LP|filter&vkgl&clinVar&gnomad&effect&sift&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||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.92206705||||||||22:50721546-50721546|4.49665e-06|0|||||LP|filter&vkgl&clinVar&gnomad&effect&sift&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||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.92206705||||||||22:50721546-50721546|4.49665e-06|0|||||LP|filter&vkgl&clinVar&gnomad&effect&sift&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||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.92206705||||||||22:50721546-50721546|4.49665e-06|0|||||LP|filter&vkgl&clinVar&gnomad&effect&sift&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||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.92206705||||||||22:50721546-50721546|4.49665e-06|0|||||LP|filter&vkgl&clinVar&gnomad&effect&sift&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||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.92206705||||||||22:50721546-50721546|4.49665e-06|0|||||LP|filter&vkgl&clinVar&gnomad&effect&sift&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||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.92206705||||||||22:50721546-50721546|4.49665e-06|0|||||LP|filter&vkgl&clinVar&gnomad&effect&sift&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||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.92206705||||||||22:50721546-50721546|4.49665e-06|0|||||LP|filter&vkgl&clinVar&gnomad&effect&sift&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||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.92206705||||||||22:50721546-50721546|4.49665e-06|0|||||LP|filter&vkgl&clinVar&gnomad&effect&sift&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||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.92206705||||||||22:50721546-50721546|4.49665e-06|0|||||LP|filter&vkgl&clinVar&gnomad&effect&sift&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||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.92206705||||||||22:50721546-50721546|4.49665e-06|0|||||LP|filter&vkgl&clinVar&gnomad&effect&sift&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||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.92206705||||||||22:50721546-50721546|4.49665e-06|0|||||LP|filter&vkgl&clinVar&gnomad&effect&sift&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||||||||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.14842245||||||||22:50721546-50721546|4.49665e-06|0|||||VUS|filter&vkgl&clinVar&gnomad&effect&sift&polyphen&impact&exit_vus|,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||||||||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.14842245||||||||22:50721546-50721546|4.49665e-06|0|||||VUS|filter&vkgl&clinVar&gnomad&effect&sift&polyphen&impact&exit_vus|,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||||||||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.14842245||||||||22:50721546-50721546|4.49665e-06|0|||||VUS|filter&vkgl&clinVar&gnomad&effect&sift&polyphen&impact&exit_vus|,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||||||||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.14842245||||||||22:50721546-50721546|4.49665e-06|0|||||VUS|filter&vkgl&clinVar&gnomad&effect&sift&polyphen&impact&exit_vus|,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||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.92206705||||||||22:50721546-50721546|4.49665e-06|0|||||LP|filter&vkgl&clinVar&gnomad&effect&sift&exit_lp| GT:AD:DP:VI:VIC:VID:VIM:GQ 1|1:0,50:50:AR:.:1:0:50 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
110
- 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|0.9700852|HP:0000951||XL|LP|||||||||||LP|filter&vkgl&exit_lp|,T|splice_donor_variant|HIGH|WDR45|11152|Transcript|NM_007075.4|protein_coding||10/11|NM_007075.4:c.830+2T>A|||||||CS135341|1||-1||1|EntrezGene||||||||||1||||||||27|28|-2|2|0.02|0.00|0.01|0.99|WDR45|VUS|0.9700852|HP:0000951||XL|LP|||||||||||LP|filter&vkgl&exit_lp|,T|upstream_gene_variant|MODIFIER|PRAF2|11230|Transcript|NM_007213.3|protein_coding||||||||||CS135341|1|1360|-1|||EntrezGene||||||||||1||||||||27|28|-2|2|0.02|0.00|0.01|0.99|WDR45|VUS|0.0149048455|||||||||||||||LP|filter&vkgl&clinVar&gnomad&effect&spliceAI&exit_lp| GT:AD:DP:VIC:VID:VIM:GQ 1|0:25,25:50:.:1:0:50 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
111
- 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|0.8890525|||||||||||9753|Pathogenic||no_assertion_criteria_provided|LP|filter&vkgl&clinVar&exit_lp| GT:AD:DP:VIC:VID:VIM:GQ 1:50:50:.:1:0:50 0:.:10:.:.:.:50 .:.:.:.:.:.:50 .:.:.:.:.:.:50 1:50:50:.:.:.:50 1:50:50:.:.:.:50
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:1:64802:0: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
+ 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
+ 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:.:.:.:.:.:.:.:.
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:.:.:.:.:.:.
104
+ 1 17355094 . C T . PASS CSQ=T|splice_donor_variant|HIGH|SDHB|6390|Transcript|NM_003000.3|protein_coding||4/7|NM_003000.3:c.423+1G>A|||||||rs398122805&CS056774&CS062098&COSV64965540|1||-1||1|EntrezGene||||||||pathogenic|0&0&0&1|1&1&1&1|21348866&17667967&17804857&16405730&21565294&15383933||||||||-49|12|26|1|0.00|0.00|0.14|0.97|SDHB|VUS|0.991252||||||HP:0000951||2.452||AD&AR||LP||||7.131000|1:17355094-17355094|1.19344e-05|0|29896|Pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|chrom&gene&filter&vkgl&exit_lp;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIG:VIM:VIPC_S:VIPP_S 1|0:5,45:50:50:AD:1:6390:1:OK:HR&GQ&DP&VIM&exit_ok 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.
105
+ 1 152520788 symbolic1 A <DEL> . PASS CSQ=deletion|transcript_ablation|HIGH|LCE3D|84648|Transcript|NM_032563.2|protein_coding|||||||||||1||-1||1|EntrezGene|||||||||||||||||||||||||||||||||||||||||||||||||||||VUS|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&annotSV&spliceAI&utr5&capice&exit_vus,deletion|upstream_gene_variant|MODIFIER|LCE3C|353144|Transcript|NM_178434.3|protein_coding|||||||||||1|2608|1|||EntrezGene|||||||||||||||||||||||||||||||||||||||||||||||||||||VUS|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&annotSV&spliceAI&utr5&capice&exit_vus,deletion|transcript_ablation|HIGH|LCE3E|353145|Transcript|NM_178435.4|protein_coding|||||||||||1||-1|||EntrezGene|||||||||||||||||||||||||||||||||||||||||||||||||||||VUS|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&annotSV&spliceAI&utr5&capice&exit_vus,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000946440||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001787329||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000013752||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000946442||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000946443||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001505919||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001787330||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001787331||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001787332||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00701519957||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00905971885||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00522719201||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm;SVLEN=-49314;SVTYPE=DEL;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIM:VIPC_S:VIPP_S 1|1:0,50:50:50:AR:1:0:OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK:HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok 0|0:50,0:50:50:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:. 1|0:25,25:50:50:.:.:.:.:.
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:1:64802:0: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:.:.:.:.:.:.
107
+ 2 6693415 . T <DEL> . PASS CSQ=deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001914803||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524064657||||||||||||1||||1|||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524052275||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524121752||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524688093||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00525576244||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524108762||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524259723||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524175972||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524198224||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524134566||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00769910345||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524344258||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524278495||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524312437||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524083163||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524770333||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00829572188||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524396085||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00909212078||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524214908||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524150456||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524239498||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00524095954||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00530094654||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm,deletion|intergenic_variant|MODIFIER||||||||||||||||1|||||||||||||||||||||||||||||||||||||||||||||||3|1B_(cf_Gene_count%2C_RE_gene%2C_-0.60)%3B2B_(cf_po_P_loss_source%2C_HI_and_OMIM_morbid%2C_+0.00)%3B3A_(0_gene%2C_+0.00)%3B5F_(+0.00)|-0.6|||||||||LQ|chrom&gene&exit_rm;END=6707844;SVLEN=-14429;SVTYPE=DEL;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIG:VIM:VIPC_S:VIPP_S 1|1:0,50:50:50:AR:1:64802:0:OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK,OK:HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok,HR&GQ&DP&VIM&VID&exit_ok 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.
108
+ 4 106320294 . G A . PASS CSQ=A|missense_variant|MODERATE|PPA2|27068|Transcript|NM_006903.4|protein_coding|7/11||NM_006903.4:c.596C>T|NP_008834.3:p.Pro199Leu|616/1586|596/918|199/305|P/L|cCg/cTg|rs138215926&CM1610192&COSV58994362|1||-1|||EntrezGene|||||0|0.985||pathogenic|0&0&1|1&1&1|27523597|||||||98|-34|27|-2|-43|0.00|0.00|0.00|0.00|PPA2|VUS|0.7474259||||||||-1.922||AR||LP||||9.359000|4:106320294-106320294|0.000211803|0|372226|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|chrom&gene&filter&vkgl&exit_lp,A|missense_variant|MODERATE|PPA2|27068|Transcript|NM_176866.2|protein_coding|4/8||NM_176866.2:c.377C>T|NP_789842.2:p.Pro126Leu|397/1367|377/699|126/232|P/L|cCg/cTg|rs138215926&CM1610192&COSV58994362|1||-1|||EntrezGene|||||0|0.992||pathogenic|0&0&1|1&1&1|27523597|||||||98|-34|27|-2|-43|0.00|0.00|0.00|0.00|PPA2|VUS|0.75460654||||||||-1.922||AR||LP||||9.359000|4:106320294-106320294|0.000211803|0|372226|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|chrom&gene&filter&vkgl&exit_lp,A|missense_variant|MODERATE|PPA2|27068|Transcript|NM_176867.3|protein_coding|2/6||NM_176867.3:c.185C>T|NP_789843.2:p.Pro62Leu|205/1175|185/507|62/168|P/L|cCg/cTg|rs138215926&CM1610192&COSV58994362|1||-1|||EntrezGene|||||0|0.995||pathogenic|0&0&1|1&1&1|27523597|||||||98|-34|27|-2|-43|0.00|0.00|0.00|0.00|PPA2|VUS|0.89774835||||||||-1.922||AR||LP||||9.359000|4:106320294-106320294|0.000211803|0|372226|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|chrom&gene&filter&vkgl&exit_lp,A|missense_variant|MODERATE|PPA2|27068|Transcript|NM_176869.3|protein_coding|8/12||NM_176869.3:c.683C>T|NP_789845.1:p.Pro228Leu|695/1665|683/1005|228/334|P/L|cCg/cTg|rs138215926&CM1610192&COSV58994362|1||-1||1|EntrezGene|||||0|0.993||pathogenic|0&0&1|1&1&1|27523597|||||||98|-34|27|-2|-43|0.00|0.00|0.00|0.00|PPA2|VUS|0.77676606||||||||-1.922||AR||LP||||9.359000|4:106320294-106320294|0.000211803|0|372226|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|chrom&gene&filter&vkgl&exit_lp,A|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001994744|promoter_flanking_region||||||||||rs138215926&CM1610192&COSV58994362|1|||||||||||||pathogenic|0&0&1|1&1&1|27523597||||||||||||||||||||||||||||||||||9.359000|4:106320294-106320294|0.000211803|0|372226|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LQ|chrom&gene&exit_rm;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIG:VIM:VIPC_S:VIPP_S 1|1:0,50:50:50:AR:1:27068:1: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 1|0:25,25:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 1|1:0,50:50:50:.:.:.:.:.:.
109
+ 9 107546633 . AAAGAT A . PASS CSQ=-|frameshift_variant|HIGH|ABCA1|19|Transcript|NM_005502.4|protein_coding|50/50||NM_005502.4:c.6744_6748del|NP_005493.2:p.Phe2250ThrfsTer3|7057-7061/10408|6744-6748/6786|2248-2250/2261|TSF/TX|acATCTTtt/actt||1||-1||1|EntrezGene||||||||||||||||||||||||||||VUS|0.97944254|||||||LC|4.243||AD&AR||||||||||||||LP|chrom&gene&filter&vkgl&clinVar&gnomAD&sv&spliceAI&utr5&capice&exit_lp;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIG:VIM:VIPC_S:VIPP_S 1|1:0,10:10:.:AR:0:19:1:OK:HR&GQ&DP&VIM&exit_ok 0|1:1,49:50:50:.:.:.:.:.:. 1|0:0,50:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.
110
+ 9 107584864 . AC A . PASS CSQ=-|frameshift_variant|HIGH|ABCA1|19|Transcript|NM_005502.4|protein_coding|19/50||NM_005502.4:c.2740del|NP_005493.2:p.Val914TrpfsTer8|3053/10408|2740/6786|914/2261|V/X|Gtg/tg||1||-1||1|EntrezGene|||||||||||||||||||33|-42|28|1|0.00|0.00|0.10|0.00|ABCA1|VUS|0.998016||||||HP:0000951|LC|4.243||AD&AR||LP||||4.010000||||||||LP|chrom&gene&filter&vkgl&exit_lp;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIG:VIM:VIPC_S:VIPP_S 1|0:10,90:50:50:AD:1:19:1:OK: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:.:.:.:.:.:.
111
+ 9 107584865 . C G . PASS CSQ=-|frameshift_variant|HIGH|ABCA1|19|Transcript|NM_005502.4|protein_coding|19/50||NM_005502.4:c.2740del|NP_005493.2:p.Val914TrpfsTer8|3053/10408|2740/6786|914/2261|V/X|Gtg/tg||1||-1||1|EntrezGene|||||||||||||||||||33|-42|28|1|0.00|0.00|0.10|0.00|ABCA1|VUS|0.998016||||||HP:0003124|HC|4.243||AD&AR||LP||||4.010000||||||||LP|chrom&gene&filter&vkgl&exit_lp;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIG:VIM:VIPC_S:VIPP_S 1|0:10,90:50:50:AD:1:19:1:OK: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:.:.:.:.:.:.
112
+ 10 126091499 . G C . PASS CSQ=C|stop_gained|HIGH|OAT|4942|Transcript|NM_000274.4|protein_coding|7/10||NM_000274.4:c.897C>G|NP_000265.1:p.Tyr299Ter|977/2039|897/1320|299/439|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808||||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.9327103||||||||-1.183||AR||LP||||1.254000|10:126091499-126091499|1.59133e-05|0|176|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|chrom&gene&filter&vkgl&exit_lp,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001171814.2|protein_coding|6/9||NM_001171814.2:c.483C>G|NP_001165285.1:p.Tyr161Ter|749/1811|483/906|161/301|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808||||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.98210585||||||||-1.183||AR||LP||||1.254000|10:126091499-126091499|1.59133e-05|0|176|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|chrom&gene&filter&vkgl&exit_lp,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322965.2|protein_coding|7/10||NM_001322965.2:c.897C>G|NP_001309894.1:p.Tyr299Ter|972/2034|897/1320|299/439|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808||||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.9327103||||||||-1.183||AR||LP||||1.254000|10:126091499-126091499|1.59133e-05|0|176|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|chrom&gene&filter&vkgl&exit_lp,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322966.2|protein_coding|8/11||NM_001322966.2:c.897C>G|NP_001309895.1:p.Tyr299Ter|1292/2354|897/1320|299/439|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1||1|EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808||||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.97306395||||||||-1.183||AR||LP||||1.254000|10:126091499-126091499|1.59133e-05|0|176|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|chrom&gene&filter&vkgl&exit_lp,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322967.2|protein_coding|8/11||NM_001322967.2:c.897C>G|NP_001309896.1:p.Tyr299Ter|1097/2159|897/1320|299/439|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808||||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.9656282||||||||-1.183||AR||LP||||1.254000|10:126091499-126091499|1.59133e-05|0|176|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|chrom&gene&filter&vkgl&exit_lp,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322968.2|protein_coding|9/12||NM_001322968.2:c.897C>G|NP_001309897.1:p.Tyr299Ter|1184/2246|897/1320|299/439|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808||||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.96872944||||||||-1.183||AR||LP||||1.254000|10:126091499-126091499|1.59133e-05|0|176|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|chrom&gene&filter&vkgl&exit_lp,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322969.2|protein_coding|8/11||NM_001322969.2:c.897C>G|NP_001309898.1:p.Tyr299Ter|1064/2126|897/1320|299/439|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808||||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.9635119||||||||-1.183||AR||LP||||1.254000|10:126091499-126091499|1.59133e-05|0|176|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|chrom&gene&filter&vkgl&exit_lp,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322970.2|protein_coding|9/12||NM_001322970.2:c.897C>G|NP_001309899.1:p.Tyr299Ter|1280/2342|897/1320|299/439|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808||||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.97306395||||||||-1.183||AR||LP||||1.254000|10:126091499-126091499|1.59133e-05|0|176|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|chrom&gene&filter&vkgl&exit_lp,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322971.2|protein_coding|5/8||NM_001322971.2:c.576C>G|NP_001309900.1:p.Tyr192Ter|656/1718|576/999|192/332|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808||||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.96748227||||||||-1.183||AR||LP||||1.254000|10:126091499-126091499|1.59133e-05|0|176|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|chrom&gene&filter&vkgl&exit_lp,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322974.2|protein_coding|7/10||NM_001322974.2:c.297C>G|NP_001309903.1:p.Tyr99Ter|863/1925|297/720|99/239|Y/*|taC/taG|rs121965057&CM920525&COSV64348333|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1|1609808||||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.96553046||||||||-1.183||AR||LP||||1.254000|10:126091499-126091499|1.59133e-05|0|176|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|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:1:4942:1:OK,OK,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,HR&GQ&DP&VIM&exit_ok,HR&GQ&DP&VIM&exit_ok 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:.:.:.:.:.:.
113
+ 13 77570128 . G A . PASS CSQ=A|missense_variant|MODERATE|CLN5|1203|Transcript|NM_001366624.2|protein_coding|3/5||NM_001366624.2:c.431G>A|NP_001353553.1:p.Cys144Tyr|449/5286|431/594|144/197|C/Y|tGt/tAt|rs1566219136|1||1|||EntrezGene|||||0|0.995||pathogenic||1||||||||194|-27|-43|-27|-1|0.00|0.00|0.01|0.00|CLN5|VUS|0.9957157||||||||1.166||AR||LP||||9.873000||||623394|Pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|chrom&gene&filter&vkgl&exit_lp,A|missense_variant|MODERATE|CLN5|1203|Transcript|NM_006493.4|protein_coding|3/4||NM_006493.4:c.431G>A|NP_006484.2:p.Cys144Tyr|449/5243|431/1077|144/358|C/Y|tGt/tAt|rs1566219136|1||1||1|EntrezGene|||||0|0.999||pathogenic||1||||||||194|-27|-43|-27|-1|0.00|0.00|0.01|0.00|CLN5|VUS|0.99436617||||||||1.166||AR||LP||||9.873000||||623394|Pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|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:.:.:.:. 0|0:50,0:50:50:.:.:.:. 0|0:50,0:50:50:.:.:.:. 0|0:50,0:50:50:.:.:.:.
114
+ 14 89307838 . C T . PASS CSQ=T|stop_gained|HIGH|TTC8|123016|Transcript|NM_001288781.1|protein_coding|6/16||NM_001288781.1:c.529C>T|NP_001275710.1:p.Gln177Ter|725/2378|529/1596|177/531|Q/*|Cag/Tag|rs376035653|1||1||1|EntrezGene|||||||||||||||||||3|-22|-8|20|0.00|0.00|0.00|0.05|TTC8|VUS|0.9826843||||||HP:0000951||1.263||AR||LP||||3.737000|14:89307838-89307838|3.99307e-06|0|997900|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|chrom&gene&filter&vkgl&exit_lp,T|5_prime_UTR_variant|MODIFIER|TTC8|123016|Transcript|NM_001288782.1|protein_coding|6/14||NM_001288782.1:c.-34C>T||725/2298|||||rs376035653|1||1|||EntrezGene|||||||||||||||||||3|-22|-8|20|0.00|0.00|0.00|0.05|TTC8|VUS|0.007844023|0|1|17|uSTOP_gained_Evidence:False&uSTOP_gained_KozakContext:GCCATGA&uSTOP_gained_KozakStrength:Moderate&uSTOP_gained_newSTOPDistanceToCDS:34&uSTOP_gained_ref_StartDistanceToCDS:562&uSTOP_gained_ref_type:uORF&uSTOP_gained_Evidence:False&uSTOP_gained_KozakContext:GAGATGG&uSTOP_gained_KozakStrength:Strong&uSTOP_gained_newSTOPDistanceToCDS:34&uSTOP_gained_ref_StartDistanceToCDS:550&uSTOP_gained_ref_type:uORF&uSTOP_gained_Evidence:False&uSTOP_gained_KozakContext:CAGATGC&uSTOP_gained_KozakStrength:Weak&uSTOP_gained_newSTOPDistanceToCDS:34&uSTOP_gained_ref_StartDistanceToCDS:475&uSTOP_gained_ref_type:uORF&uSTOP_gained_Evidence:False&uSTOP_gained_KozakContext:GAAATGG&uSTOP_gained_KozakStrength:Strong&uSTOP_gained_newSTOPDistanceToCDS:34&uSTOP_gained_ref_StartDistanceToCDS:412&uSTOP_gained_ref_type:uORF&uSTOP_gained_Evidence:False&uSTOP_gained_KozakContext:GAAATGA&uSTOP_gained_KozakStrength:Moderate&uSTOP_gained_newSTOPDistanceToCDS:34&uSTOP_gained_ref_StartDistanceToCDS:364&uSTOP_gained_ref_type:uORF&uSTOP_gained_Evidence:False&uSTOP_gained_KozakContext:ATGATGC&uSTOP_gained_KozakStrength:Moderate&uSTOP_gained_newSTOPDistanceToCDS:34&uSTOP_gained_ref_StartDistanceToCDS:361&uSTOP_gained_ref_type:uORF&uSTOP_gained_Evidence:False&uSTOP_gained_KozakContext:ACTATGG&uSTOP_gained_KozakStrength:Strong&uSTOP_gained_newSTOPDistanceToCDS:34&uSTOP_gained_ref_StartDistanceToCDS:190&uSTOP_gained_ref_type:uORF&uSTOP_gained_Evidence:False&uSTOP_gained_KozakContext:TCCATGC&uSTOP_gained_KozakStrength:Weak&uSTOP_gained_newSTOPDistanceToCDS:34&uSTOP_gained_ref_StartDistanceToCDS:97&uSTOP_gained_ref_type:uORF|uSTOP_gained&uSTOP_gained&uSTOP_gained&uSTOP_gained&uSTOP_gained&uSTOP_gained&uSTOP_gained&uSTOP_gained|HP:0000951||1.263||AR||LP||||3.737000|14:89307838-89307838|3.99307e-06|0|997900|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|chrom&gene&filter&vkgl&exit_lp,T|intron_variant|MODIFIER|TTC8|123016|Transcript|NM_001288783.1|protein_coding||5/14|NM_001288783.1:c.-199+298C>T|||||||rs376035653|1||1|||EntrezGene|||||||||||||||||||3|-22|-8|20|0.00|0.00|0.00|0.05|TTC8|VUS|0.065462574||||||HP:0000951||1.263||AR||LP||||3.737000|14:89307838-89307838|3.99307e-06|0|997900|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|chrom&gene&filter&vkgl&exit_lp,T|stop_gained|HIGH|TTC8|123016|Transcript|NM_001366535.2|protein_coding|5/13||NM_001366535.2:c.529C>T|NP_001353464.1:p.Gln177Ter|586/5160|529/1434|177/477|Q/*|Cag/Tag|rs376035653|1||1|||EntrezGene|||||||||||||||||||3|-22|-8|20|0.00|0.00|0.00|0.05|TTC8|VUS|0.9942367||||||HP:0000951||1.263||AR||LP||||3.737000|14:89307838-89307838|3.99307e-06|0|997900|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|chrom&gene&filter&vkgl&exit_lp,T|intron_variant|MODIFIER|TTC8|123016|Transcript|NM_001366536.2|protein_coding||4/11|NM_001366536.2:c.459+298C>T|||||||rs376035653|1||1|||EntrezGene|||||||||||||||||||3|-22|-8|20|0.00|0.00|0.00|0.05|TTC8|VUS|0.065462574||||||HP:0000951||1.263||AR||LP||||3.737000|14:89307838-89307838|3.99307e-06|0|997900|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|chrom&gene&filter&vkgl&exit_lp,T|stop_gained|HIGH|TTC8|123016|Transcript|NM_144596.4|protein_coding|6/15||NM_144596.4:c.559C>T|NP_653197.2:p.Gln187Ter|616/2183|559/1548|187/515|Q/*|Cag/Tag|rs376035653|1||1|||EntrezGene|||||||||||||||||||3|-22|-8|20|0.00|0.00|0.00|0.05|TTC8|VUS|0.9777649||||||HP:0000951||1.263||AR||LP||||3.737000|14:89307838-89307838|3.99307e-06|0|997900|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|chrom&gene&filter&vkgl&exit_lp,T|stop_gained|HIGH|TTC8|123016|Transcript|NM_198309.3|protein_coding|6/15||NM_198309.3:c.529C>T|NP_938051.1:p.Gln177Ter|725/2300|529/1518|177/505|Q/*|Cag/Tag|rs376035653|1||1|||EntrezGene|||||||||||||||||||3|-22|-8|20|0.00|0.00|0.00|0.05|TTC8|VUS|0.9769935||||||HP:0000951||1.263||AR||LP||||3.737000|14:89307838-89307838|3.99307e-06|0|997900|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|chrom&gene&filter&vkgl&exit_lp,T|intron_variant|MODIFIER|TTC8|123016|Transcript|NM_198310.3|protein_coding||5/13|NM_198310.3:c.459+298C>T|||||||rs376035653|1||1|||EntrezGene|||||||||||||||||||3|-22|-8|20|0.00|0.00|0.00|0.05|TTC8|VUS|0.065462574||||||HP:0000951||1.263||AR||LP||||3.737000|14:89307838-89307838|3.99307e-06|0|997900|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|chrom&gene&filter&vkgl&exit_lp,T|non_coding_transcript_exon_variant|MODIFIER|TTC8|123016|Transcript|NR_159362.2|misc_RNA|5/15||NR_159362.2:n.586C>T||586/5304|||||rs376035653|1||1|||EntrezGene|||||||||||||||||||3|-22|-8|20|0.00|0.00|0.00|0.05|TTC8|VUS|0.0989985||||||HP:0000951||1.263||AR||LP||||3.737000|14:89307838-89307838|3.99307e-06|0|997900|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|chrom&gene&filter&vkgl&exit_lp,T|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001864166|enhancer||||||||||rs376035653|1||||||||||||||||||||||||||||||||||||||||||||||||||3.737000|14:89307838-89307838|3.99307e-06|0|997900|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LQ|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,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 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:.:.:.:.:.
115
+ 14 89310195 . G A . PASS CSQ=A|splice_donor_variant|HIGH|TTC8|123016|Transcript|NM_001288781.1|protein_coding||7/15|NM_001288781.1:c.594+1G>A|||||||rs587777808&CD056477&CS056440|1||1||1|EntrezGene||||||||pathogenic||1&1&1|16308660||||||||32|-45|32|-1|0.00|0.00|0.00|1.00|TTC8|VUS|0.9902351||||||HP:0000951||1.263||AR||LP||||8.399000||||2531|Pathogenic||no_assertion_criteria_provided|LP|chrom&gene&filter&vkgl&exit_lp,A|intron_variant|MODIFIER|TTC8|123016|Transcript|NM_001288782.1|protein_coding||6/13|NM_001288782.1:c.30+2294G>A|||||||rs587777808&CD056477&CS056440|1||1|||EntrezGene||||||||pathogenic||1&1&1|16308660||||||||32|-45|32|-1|0.00|0.00|0.00|1.00|TTC8|VUS|0.8040881||||||HP:0000951||1.263||AR||LP||||8.399000||||2531|Pathogenic||no_assertion_criteria_provided|LP|chrom&gene&filter&vkgl&exit_lp,A|splice_donor_variant|HIGH|TTC8|123016|Transcript|NM_001288783.1|protein_coding||6/14|NM_001288783.1:c.-154+1G>A|||||||rs587777808&CD056477&CS056440|1||1|||EntrezGene||||||||pathogenic||1&1&1|16308660||||||||32|-45|32|-1|0.00|0.00|0.00|1.00|TTC8|VUS|0.9902351||||||HP:0000951||1.263||AR||LP||||8.399000||||2531|Pathogenic||no_assertion_criteria_provided|LP|chrom&gene&filter&vkgl&exit_lp,A|splice_donor_variant|HIGH|TTC8|123016|Transcript|NM_001366535.2|protein_coding||6/12|NM_001366535.2:c.594+1G>A|||||||rs587777808&CD056477&CS056440|1||1|||EntrezGene||||||||pathogenic||1&1&1|16308660||||||||32|-45|32|-1|0.00|0.00|0.00|1.00|TTC8|VUS|0.9902351||||||HP:0000951||1.263||AR||LP||||8.399000||||2531|Pathogenic||no_assertion_criteria_provided|LP|chrom&gene&filter&vkgl&exit_lp,A|splice_donor_variant|HIGH|TTC8|123016|Transcript|NM_001366536.2|protein_coding||5/11|NM_001366536.2:c.504+1G>A|||||||rs587777808&CD056477&CS056440|1||1|||EntrezGene||||||||pathogenic||1&1&1|16308660||||||||32|-45|32|-1|0.00|0.00|0.00|1.00|TTC8|VUS|0.9902351||||||HP:0000951||1.263||AR||LP||||8.399000||||2531|Pathogenic||no_assertion_criteria_provided|LP|chrom&gene&filter&vkgl&exit_lp,A|splice_donor_variant|HIGH|TTC8|123016|Transcript|NM_144596.4|protein_coding||7/14|NM_144596.4:c.624+1G>A|||||||rs587777808&CD056477&CS056440|1||1|||EntrezGene||||||||pathogenic||1&1&1|16308660||||||||32|-45|32|-1|0.00|0.00|0.00|1.00|TTC8|VUS|0.9902351||||||HP:0000951||1.263||AR||LP||||8.399000||||2531|Pathogenic||no_assertion_criteria_provided|LP|chrom&gene&filter&vkgl&exit_lp,A|splice_donor_variant|HIGH|TTC8|123016|Transcript|NM_198309.3|protein_coding||7/14|NM_198309.3:c.594+1G>A|||||||rs587777808&CD056477&CS056440|1||1|||EntrezGene||||||||pathogenic||1&1&1|16308660||||||||32|-45|32|-1|0.00|0.00|0.00|1.00|TTC8|VUS|0.9902351||||||HP:0000951||1.263||AR||LP||||8.399000||||2531|Pathogenic||no_assertion_criteria_provided|LP|chrom&gene&filter&vkgl&exit_lp,A|splice_donor_variant|HIGH|TTC8|123016|Transcript|NM_198310.3|protein_coding||6/13|NM_198310.3:c.504+1G>A|||||||rs587777808&CD056477&CS056440|1||1|||EntrezGene||||||||pathogenic||1&1&1|16308660||||||||32|-45|32|-1|0.00|0.00|0.00|1.00|TTC8|VUS|0.9902351||||||HP:0000951||1.263||AR||LP||||8.399000||||2531|Pathogenic||no_assertion_criteria_provided|LP|chrom&gene&filter&vkgl&exit_lp,A|splice_donor_variant&non_coding_transcript_variant|HIGH|TTC8|123016|Transcript|NR_159362.2|misc_RNA||6/14|NR_159362.2:n.651+1G>A|||||||rs587777808&CD056477&CS056440|1||1|||EntrezGene||||||||pathogenic||1&1&1|16308660||||||||32|-45|32|-1|0.00|0.00|0.00|1.00|TTC8|VUS|0.9901416||||||HP:0000951||1.263||AR||LP||||8.399000||||2531|Pathogenic||no_assertion_criteria_provided|LP|chrom&gene&filter&vkgl&exit_lp;VIPC_S=LQ GT:AD:DP:GQ:VI:VID:VIG:VIM:VIPC_S:VIPP_S 1|1:0,9:9:50:AR:0:123016:1:LQ,LQ,LQ,LQ,LQ,LQ,LQ,LQ,LQ:HR&GQ&DP&exit_lq,HR&GQ&DP&exit_lq,HR&GQ&DP&exit_lq,HR&GQ&DP&exit_lq,HR&GQ&DP&exit_lq,HR&GQ&DP&exit_lq,HR&GQ&DP&exit_lq,HR&GQ&DP&exit_lq,HR&GQ&DP&exit_lq 0|1:.:10:50:.:.:.:.:.:. 0|1:50:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.
116
+ 14 89336407 . TG T . PASS CSQ=-|frameshift_variant|HIGH|TTC8|123016|Transcript|NM_001288781.1|protein_coding|12/16||NM_001288781.1:c.963del|NP_001275710.1:p.Met321IlefsTer15|1159/2378|963/1596|321/531|M/X|atG/at|rs1431207606|1||1||1|EntrezGene|||||||||||||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.9979407||||||HP:0000951||1.263||AR||LP||||9.393000|14:89336408-89336409|1.19537e-05|0|930561|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|chrom&gene&filter&vkgl&exit_lp,-|frameshift_variant|HIGH|TTC8|123016|Transcript|NM_001288782.1|protein_coding|10/14||NM_001288782.1:c.321del|NP_001275711.1:p.Met107IlefsTer15|1079/2298|321/954|107/317|M/X|atG/at|rs1431207606|1||1|||EntrezGene|||||||||||||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.9975501||||||HP:0000951||1.263||AR||LP||||9.393000|14:89336408-89336409|1.19537e-05|0|930561|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|chrom&gene&filter&vkgl&exit_lp,-|frameshift_variant|HIGH|TTC8|123016|Transcript|NM_001288783.1|protein_coding|11/15||NM_001288783.1:c.198del|NP_001275712.1:p.Met66IlefsTer15|1051/2270|198/831|66/276|M/X|atG/at|rs1431207606|1||1|||EntrezGene|||||||||||||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.9940432||||||HP:0000951||1.263||AR||LP||||9.393000|14:89336408-89336409|1.19537e-05|0|930561|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|chrom&gene&filter&vkgl&exit_lp,-|frameshift_variant|HIGH|TTC8|123016|Transcript|NM_001366535.2|protein_coding|10/13||NM_001366535.2:c.885del|NP_001353464.1:p.Met295IlefsTer15|942/5160|885/1434|295/477|M/X|atG/at|rs1431207606|1||1|||EntrezGene|||||||||||||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.99769527||||||HP:0000951||1.263||AR||LP||||9.393000|14:89336408-89336409|1.19537e-05|0|930561|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|chrom&gene&filter&vkgl&exit_lp,-|frameshift_variant|HIGH|TTC8|123016|Transcript|NM_001366536.2|protein_coding|9/12||NM_001366536.2:c.795del|NP_001353465.1:p.Met265IlefsTer15|852/5070|795/1344|265/447|M/X|atG/at|rs1431207606|1||1|||EntrezGene|||||||||||||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.9988078||||||HP:0000951||1.263||AR||LP||||9.393000|14:89336408-89336409|1.19537e-05|0|930561|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|chrom&gene&filter&vkgl&exit_lp,-|frameshift_variant|HIGH|TTC8|123016|Transcript|NM_144596.4|protein_coding|11/15||NM_144596.4:c.915del|NP_653197.2:p.Met305IlefsTer15|972/2183|915/1548|305/515|M/X|atG/at|rs1431207606|1||1|||EntrezGene|||||||||||||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.99404776||||||HP:0000951||1.263||AR||LP||||9.393000|14:89336408-89336409|1.19537e-05|0|930561|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|chrom&gene&filter&vkgl&exit_lp,-|frameshift_variant|HIGH|TTC8|123016|Transcript|NM_198309.3|protein_coding|11/15||NM_198309.3:c.885del|NP_938051.1:p.Met295IlefsTer15|1081/2300|885/1518|295/505|M/X|atG/at|rs1431207606|1||1|||EntrezGene|||||||||||||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.9971411||||||HP:0000951||1.263||AR||LP||||9.393000|14:89336408-89336409|1.19537e-05|0|930561|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|chrom&gene&filter&vkgl&exit_lp,-|frameshift_variant|HIGH|TTC8|123016|Transcript|NM_198310.3|protein_coding|10/14||NM_198310.3:c.795del|NP_938052.1:p.Met265IlefsTer15|991/2210|795/1428|265/475|M/X|atG/at|rs1431207606|1||1|||EntrezGene|||||||||||||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.9968329||||||HP:0000951||1.263||AR||LP||||9.393000|14:89336408-89336409|1.19537e-05|0|930561|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|chrom&gene&filter&vkgl&exit_lp,-|non_coding_transcript_exon_variant|MODIFIER|TTC8|123016|Transcript|NR_159362.2|misc_RNA|11/15||NR_159362.2:n.1002del||1002/5304|||||rs1431207606|1||1|||EntrezGene|||||||||||||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.6298463||||||HP:0000951||1.263||AR||LP||||9.393000|14:89336408-89336409|1.19537e-05|0|930561|Pathogenic/Likely_pathogenic||criteria_provided&_multiple_submitters&_no_conflicts|LP|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:1:123016:1:OK,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,HR&GQ&DP&VIM&exit_ok 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:.:.:.:.:.:.
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
+ 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
+ 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:.:.:.:.:.:.:.
121
+ 17 29683983 . C T . PASS CSQ=T|stop_gained|HIGH|NF1|4763|Transcript|NM_000267.3|protein_coding|52/57||NM_000267.3:c.7681C>T|NP_000258.1:p.Gln2561Ter|8064/12362|7681/8457|2561/2818|Q/*|Cag/Tag|CM143479|1||1|||EntrezGene||||||||||1|||||||||24|-5|24|36|0.02|0.00|0.00|0.00|NF1|VUS|0.9976593||||||HP:0000951||0.583|1|AD||LP||||6.871000||||||||LP|chrom&gene&filter&vkgl&exit_lp,T|stop_gained|HIGH|NF1|4763|Transcript|NM_001042492.3|protein_coding|53/58||NM_001042492.3:c.7744C>T|NP_001035957.1:p.Gln2582Ter|8077/12373|7744/8520|2582/2839|Q/*|Cag/Tag|CM143479|1||1||1|EntrezGene||||||||||1|||||||||24|-5|24|36|0.02|0.00|0.00|0.00|NF1|VUS|0.9986885||||||HP:0000951||0.583|1|AD||LP||||6.871000||||||||LP|chrom&gene&filter&vkgl&exit_lp;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIG:VIM:VIPC_S:VIPP_S:VIS .|.:25,25:50:50:AR,AD:0:4763:1:OK,OK:HR&GQ&DP&VIM&exit_ok,HR&GQ&DP&VIM&exit_ok:AR_C 0|0:50,0:50:50:.:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.:.
122
+ 19 11224051 . C CGTGGTCGCTCTGGACACGGAG . PASS CSQ=TCGCTCTGGACACGGAGGTGG|inframe_insertion|MODERATE|LDLR|3949|Transcript|NM_000527.5|protein_coding|9/18||NM_000527.5:c.1289_1309dup|NP_000518.1:p.Val436_Ala437insGlyGlyArgSerGlyHisGly|1395-1396/5173|1309-1310/2583|437/860|A/VALDTEVA|gcc/gTCGCTCTGGACACGGAGGTGGcc||1||1||1|EntrezGene|||||||25|||||||||||||||||||||VUS|0.8812568|||||||HC|5.497||AD&AR||LP||||||||||||LP|chrom&gene&filter&vkgl&exit_lp;VIPC_S=OK GT:AD:DP:GQ:VI:VID:VIG:VIM:VIPC_S:VIPP_S 1|1:.:10:50:AR:0:3949:1:OK:HR&GQ&DP&VIM&exit_ok 0|1:.:10:50:.:.:.:.:.:. 1|0:25,25:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:. 0|0:50,0:50:50:.:.:.:.:.:.
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
+ 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:.:.:.:.:.
126
+ 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
+ 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
@@ -1,6 +1,14 @@
1
1
  import { Component, createMemo, createResource, Show } from "solid-js";
2
2
  import { useRouteData } from "@solidjs/router";
3
- import { HtsFileMetadata, Item, Params, PhenotypicFeature, Sample, SortPath } from "@molgenis/vip-report-api/src/Api";
3
+ import {
4
+ HtsFileMetadata,
5
+ Item,
6
+ Params,
7
+ PhenotypicFeature,
8
+ QueryClause,
9
+ Sample,
10
+ SortPath,
11
+ } from "@molgenis/vip-report-api/src/Api";
4
12
  import { Loader } from "../components/Loader";
5
13
  import { SearchBox } from "../components/SearchBox";
6
14
  import { Sort, SortEvent } from "../components/Sort";
@@ -80,15 +88,30 @@ export const SampleVariants: Component<{
80
88
 
81
89
  if (getStateVariants()?.filterQueries === undefined) {
82
90
  const hpoField = props.recordsMeta.info?.CSQ?.nested?.items?.find((field) => field.id === "HPO");
91
+ const gadoField = props.recordsMeta.info?.CSQ?.nested?.items?.find((field) => field.id === "GADO_PD");
83
92
  if (hpoField && props.samplePhenotypes.length > 0) {
84
93
  const selectorHpo = infoSelector(hpoField);
85
- actions.setSampleVariantsFilterQuery(
86
- props.sample,
94
+ const queries: QueryClause[] = [
87
95
  {
88
96
  selector: selectorHpo,
89
97
  operator: "any_has_any",
90
98
  args: props.samplePhenotypes.map((phenotype) => phenotype.type.id),
91
99
  },
100
+ ];
101
+ if (gadoField) {
102
+ const selectorGado = infoSelector(gadoField);
103
+ queries.push({
104
+ selector: selectorGado,
105
+ operator: "has_any",
106
+ args: ["HC"],
107
+ });
108
+ }
109
+ actions.setSampleVariantsFilterQuery(
110
+ props.sample,
111
+ {
112
+ operator: "or",
113
+ args: queries,
114
+ },
92
115
  selectorKey(selectorHpo)
93
116
  );
94
117
  }