@molgenis/vip-report-template 6.2.0 → 7.0.1

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Files changed (285) hide show
  1. package/.nvmrc +1 -1
  2. package/.travis.yml +9 -9
  3. package/README.md +411 -1
  4. package/eslint.config.mjs +11 -0
  5. package/package.json +40 -35
  6. package/scripts/deploy_npm_registry.sh +5 -0
  7. package/src/App.tsx +30 -24
  8. package/src/assets/sass/main.scss +12 -4
  9. package/src/components/Allele.tsx +95 -0
  10. package/src/components/Anchor.tsx +1 -1
  11. package/src/components/Breadcrumb.tsx +6 -4
  12. package/src/components/DatasetDropdown.tsx +12 -25
  13. package/src/components/ErrorNotification.tsx +9 -0
  14. package/src/components/GenomeBrowser.tsx +40 -23
  15. package/src/components/HpoTerm.tsx +1 -1
  16. package/src/components/{record/Pager.tsx → Pager.tsx} +21 -14
  17. package/src/components/RecordsPerPage.tsx +9 -7
  18. package/src/components/RecordsTable.tsx +130 -0
  19. package/src/components/SampleTable.tsx +70 -98
  20. package/src/components/SearchBox.tsx +8 -2
  21. package/src/components/Sort.tsx +28 -25
  22. package/src/components/Table.tsx +16 -0
  23. package/src/components/Tooltip.tsx +20 -0
  24. package/src/components/VariantBreadcrumb.tsx +54 -0
  25. package/src/components/VariantConsequenceContainer.tsx +100 -0
  26. package/src/components/VariantConsequenceTable.tsx +58 -0
  27. package/src/components/VariantContainer.tsx +71 -0
  28. package/src/components/VariantFilters.tsx +27 -0
  29. package/src/components/VariantGenotypeTable.tsx +44 -0
  30. package/src/components/VariantInfoTable.tsx +24 -33
  31. package/src/components/VariantResults.tsx +103 -0
  32. package/src/components/VariantTable.tsx +62 -66
  33. package/src/components/VariantTypeSelect.tsx +34 -0
  34. package/src/components/VariantsContainer.tsx +150 -0
  35. package/src/components/VariantsContainerHeader.tsx +70 -0
  36. package/src/components/field/Field.tsx +80 -0
  37. package/src/components/field/FieldAlt.tsx +19 -0
  38. package/src/components/field/FieldChrom.tsx +6 -0
  39. package/src/components/{record/Id.tsx → field/FieldFilter.tsx} +2 -1
  40. package/src/components/field/FieldFormat.tsx +10 -0
  41. package/src/components/{record/Filter.tsx → field/FieldId.tsx} +1 -1
  42. package/src/components/field/FieldPos.tsx +6 -0
  43. package/src/components/field/FieldQual.tsx +6 -0
  44. package/src/components/field/FieldRef.tsx +8 -0
  45. package/src/components/field/composed/FieldClinVar.tsx +72 -0
  46. package/src/components/field/composed/FieldComposed.tsx +68 -0
  47. package/src/components/field/composed/FieldGene.tsx +39 -0
  48. package/src/components/field/composed/FieldGenotype.tsx +35 -0
  49. package/src/components/{record/format/GenotypeField.tsx → field/composed/FieldGenotypeSnvSv.tsx} +20 -16
  50. package/src/components/field/composed/FieldGenotypeStr.tsx +31 -0
  51. package/src/components/field/composed/FieldGnomAd.tsx +58 -0
  52. package/src/components/field/composed/FieldHpo.tsx +50 -0
  53. package/src/components/field/composed/FieldInheritanceModes.tsx +32 -0
  54. package/src/components/field/composed/FieldLocus.tsx +18 -0
  55. package/src/components/field/composed/FieldVipC.tsx +25 -0
  56. package/src/components/field/composed/FieldVipCS.tsx +15 -0
  57. package/src/components/field/composed/FieldVkgl.tsx +37 -0
  58. package/src/components/field/genotype/FieldGenotype.tsx +19 -0
  59. package/src/components/field/genotype/FieldGenotypeType.tsx +9 -0
  60. package/src/components/field/info/FieldConsequence.tsx +15 -0
  61. package/src/components/{record/info/Hgvs.tsx → field/info/FieldHgvs.tsx} +4 -6
  62. package/src/components/field/info/FieldInfo.tsx +27 -0
  63. package/src/components/{record/info/PubMed.tsx → field/info/FieldPubMed.tsx} +4 -7
  64. package/src/components/field/typed/FieldCategorical.tsx +17 -0
  65. package/src/components/{record/field/FieldValueCharacter.tsx → field/typed/FieldCharacter.tsx} +3 -2
  66. package/src/components/{record/field/FieldValueFlag.tsx → field/typed/FieldFlag.tsx} +3 -2
  67. package/src/components/{record/field/FieldValueFloat.tsx → field/typed/FieldFloat.tsx} +3 -2
  68. package/src/components/{record/field/FieldValueInteger.tsx → field/typed/FieldInteger.tsx} +3 -2
  69. package/src/components/{record/field/FieldValueString.tsx → field/typed/FieldString.tsx} +3 -2
  70. package/src/components/field/typed/FieldTyped.tsx +20 -0
  71. package/src/components/field/typed/FieldTypedItem.tsx +49 -0
  72. package/src/components/field/typed/FieldTypedMultiple.tsx +21 -0
  73. package/src/components/filter/Filter.tsx +56 -48
  74. package/src/components/filter/FilterWrapper.scss +23 -0
  75. package/src/components/filter/FilterWrapper.tsx +63 -0
  76. package/src/components/filter/composed/FilterAllelicImbalance.tsx +26 -0
  77. package/src/components/filter/composed/FilterComposed.tsx +92 -0
  78. package/src/components/filter/composed/FilterDeNovo.tsx +35 -0
  79. package/src/components/filter/composed/FilterHpo.tsx +16 -0
  80. package/src/components/filter/composed/FilterInheritance.tsx +42 -0
  81. package/src/components/filter/composed/FilterLocus.tsx +75 -0
  82. package/src/components/filter/composed/FilterVipC.tsx +16 -0
  83. package/src/components/filter/composed/FilterVipCS.tsx +16 -0
  84. package/src/components/filter/fixed/FilterAlt.tsx +20 -0
  85. package/src/components/filter/fixed/FilterChrom.tsx +22 -0
  86. package/src/components/filter/fixed/FilterFilter.tsx +20 -0
  87. package/src/components/filter/fixed/FilterFixed.tsx +96 -0
  88. package/src/components/filter/fixed/FilterId.tsx +20 -0
  89. package/src/components/filter/fixed/FilterPos.tsx +22 -0
  90. package/src/components/filter/fixed/FilterQual.tsx +21 -0
  91. package/src/components/filter/fixed/FilterRef.tsx +22 -0
  92. package/src/components/filter/typed/FilterCategorical.tsx +119 -0
  93. package/src/components/filter/typed/FilterFlag.tsx +23 -0
  94. package/src/components/filter/typed/FilterInterval.tsx +72 -0
  95. package/src/components/filter/typed/FilterString.tsx +43 -0
  96. package/src/components/filter/typed/FilterTyped.tsx +56 -0
  97. package/src/components/form/ButtonApply.tsx +11 -0
  98. package/src/components/form/ButtonDownload.tsx +11 -0
  99. package/src/components/form/ButtonReset.tsx +9 -0
  100. package/src/components/{Checkbox.tsx → form/Checkbox.tsx} +4 -9
  101. package/src/components/form/Input.tsx +19 -0
  102. package/src/components/form/Select.scss +7 -0
  103. package/src/components/form/Select.tsx +34 -0
  104. package/src/components/tree/DecisionTreeBoolMultiQuery.tsx +1 -1
  105. package/src/components/tree/DecisionTreeBoolQuery.tsx +1 -1
  106. package/src/components/tree/DecisionTreeNode.tsx +41 -39
  107. package/src/components/tree/DecisionTreeNodeBool.tsx +1 -1
  108. package/src/components/tree/DecisionTreeNodeBoolMulti.tsx +1 -1
  109. package/src/components/tree/DecisionTreeNodeCategorical.tsx +1 -1
  110. package/src/components/tree/DecisionTreeNodeExists.tsx +1 -1
  111. package/src/components/tree/DecisionTreeNodeLeaf.tsx +1 -1
  112. package/src/components/tree/DecisionTreeOutcomeNode.tsx +1 -1
  113. package/src/components/tree/DecisionTreePath.tsx +1 -1
  114. package/src/igv.d.ts +2 -1
  115. package/src/index.tsx +48 -19
  116. package/src/mocks/GRCh37/decisionTree.json +23 -22
  117. package/src/mocks/GRCh37/field_metadata.json +435 -95
  118. package/src/mocks/GRCh37/sampleTree.json +21 -1
  119. package/src/mocks/GRCh37/static.ts +62 -134
  120. package/src/mocks/GRCh37/vcf/family.vcf.blob +9 -3
  121. package/src/mocks/GRCh38/decisionTree.json +52 -33
  122. package/src/mocks/GRCh38/decisionTreeStr.json +572 -0
  123. package/src/mocks/GRCh38/fasta/chr1_149380406-149403321.fasta.gz.blob +0 -0
  124. package/src/mocks/GRCh38/field_metadata.json +435 -95
  125. package/src/mocks/GRCh38/sampleTree.json +175 -0
  126. package/src/mocks/GRCh38/static.ts +101 -42
  127. package/src/mocks/GRCh38/str.cram.blob +0 -0
  128. package/src/mocks/GRCh38/str.cram.crai.blob +0 -0
  129. package/src/mocks/GRCh38/vcf/family.vcf.blob +25 -24
  130. package/src/mocks/GRCh38/vcf/no_vep.vcf.blob +29 -28
  131. package/src/mocks/GRCh38/vcf/samples_0.vcf.blob +28 -27
  132. package/src/mocks/GRCh38/vcf/samples_1.vcf.blob +29 -28
  133. package/src/mocks/GRCh38/vcf/samples_100.vcf.blob +28 -27
  134. package/src/mocks/GRCh38/vcf/str.vcf.blob +321 -0
  135. package/src/mocks/MockApiClient.ts +339 -332
  136. package/src/mocks/config_cram.json +701 -0
  137. package/src/mocks/config_vcf.json +699 -0
  138. package/src/store/app.ts +30 -0
  139. package/src/store/index.tsx +3 -168
  140. package/src/store/variants.ts +182 -0
  141. package/src/types/config.d.ts +190 -0
  142. package/src/types/configCellComposed.d.ts +86 -0
  143. package/src/types/configCells.d.ts +129 -0
  144. package/src/types/configFilter.d.ts +80 -0
  145. package/src/types/configFilterComposed.d.ts +60 -0
  146. package/src/types/configSort.d.ts +13 -0
  147. package/src/types/filter.d.ts +17 -0
  148. package/src/types/store.d.ts +34 -0
  149. package/src/utils/api.ts +281 -0
  150. package/src/utils/config/config.ts +182 -0
  151. package/src/utils/config/configCells.ts +74 -0
  152. package/src/utils/config/configCellsComposed.ts +508 -0
  153. package/src/utils/config/configCellsField.ts +61 -0
  154. package/src/utils/config/configCellsFixed.ts +126 -0
  155. package/src/utils/config/configFilters.ts +46 -0
  156. package/src/utils/config/configFiltersComposed.ts +208 -0
  157. package/src/utils/config/configFiltersField.ts +49 -0
  158. package/src/utils/config/configFiltersFixed.ts +106 -0
  159. package/src/utils/config/configSorts.ts +44 -0
  160. package/src/utils/config/configValidator.ts +380 -0
  161. package/src/utils/config/configVip.ts +25 -0
  162. package/src/utils/csq.ts +115 -0
  163. package/src/utils/decisionTree.ts +45 -0
  164. package/src/utils/download.ts +30 -0
  165. package/src/utils/error.ts +69 -0
  166. package/src/utils/query/query.ts +55 -0
  167. package/src/utils/query/queryFilter.ts +132 -0
  168. package/src/utils/query/queryFilterComposed.ts +247 -0
  169. package/src/utils/query/queryFilterField.ts +75 -0
  170. package/src/utils/query/queryFilterFixed.ts +44 -0
  171. package/src/utils/query/querySample.ts +18 -0
  172. package/src/utils/query/queryVariantType.ts +76 -0
  173. package/src/utils/query/selector.ts +41 -0
  174. package/src/utils/{sortUtils.ts → query/sort.ts} +32 -11
  175. package/src/utils/sample.ts +19 -35
  176. package/src/utils/utils.ts +66 -2
  177. package/src/utils/variantType.ts +43 -0
  178. package/src/utils/vcf.ts +352 -0
  179. package/src/views/Help.tsx +109 -114
  180. package/src/views/Home.tsx +3 -2
  181. package/src/views/Sample.tsx +12 -7
  182. package/src/views/SampleVariant.tsx +23 -112
  183. package/src/views/SampleVariantConsequence.tsx +54 -144
  184. package/src/views/SampleVariants.tsx +33 -445
  185. package/src/views/SampleVariantsRedirect.tsx +20 -0
  186. package/src/views/Samples.tsx +7 -10
  187. package/src/views/Variant.tsx +31 -61
  188. package/src/views/VariantConsequence.tsx +42 -72
  189. package/src/views/Variants.tsx +29 -138
  190. package/src/views/VariantsRedirect.tsx +25 -0
  191. package/src/views/data/data.tsx +32 -6
  192. package/tests/store/variants.test.ts +122 -0
  193. package/tests/utils/config/config.test.ts +167 -0
  194. package/tests/utils/config/configCells.test.ts +86 -0
  195. package/tests/utils/config/configCellsComposed.test.ts +1163 -0
  196. package/tests/utils/config/configCellsField.test.ts +164 -0
  197. package/tests/utils/config/configCellsFixed.test.ts +99 -0
  198. package/tests/utils/config/configFilters.test.ts +80 -0
  199. package/tests/utils/config/configFiltersComposed.test.ts +504 -0
  200. package/tests/utils/config/configFiltersField.test.ts +140 -0
  201. package/tests/utils/config/configFiltersFixed.test.ts +81 -0
  202. package/tests/utils/config/configSorts.test.ts +55 -0
  203. package/tests/utils/config/configValidator.test.ts +56 -0
  204. package/tests/utils/config/configVip.test.ts +53 -0
  205. package/tests/utils/decisionTree.test.ts +71 -0
  206. package/tests/utils/download.test.ts +20 -0
  207. package/tests/utils/query/query.test.ts +84 -0
  208. package/tests/utils/query/queryFilter.test.ts +243 -0
  209. package/tests/utils/query/queryFilterComposed.test.ts +301 -0
  210. package/tests/utils/query/queryFilterField.test.ts +75 -0
  211. package/tests/utils/query/queryFilterFixed.test.ts +86 -0
  212. package/tests/utils/query/querySample.test.ts +45 -0
  213. package/tests/utils/query/queryVariantType.test.ts +56 -0
  214. package/{src/__tests__/sortUtils.test.ts → tests/utils/query/sort.test.ts} +3 -4
  215. package/tests/utils/sample.test.ts +259 -0
  216. package/tests/utils/utils.test.ts +120 -0
  217. package/tests/utils/variantType.test.ts +48 -0
  218. package/tests/utils/vcf.test.ts +649 -0
  219. package/tsconfig.json +6 -2
  220. package/vite.config.mts +20 -3
  221. package/.eslintignore +0 -4
  222. package/.eslintrc.js +0 -23
  223. package/src/Api.ts +0 -12
  224. package/src/__tests__/decisionTreeUtils.test.ts +0 -75
  225. package/src/__tests__/field.test.ts +0 -107
  226. package/src/__tests__/query.test.ts +0 -188
  227. package/src/__tests__/sample.test.ts +0 -184
  228. package/src/__tests__/utils.test.ts +0 -24
  229. package/src/__tests__/viewUtils.test.ts +0 -125
  230. package/src/components/ConsequenceTable.tsx +0 -45
  231. package/src/components/Error.tsx +0 -9
  232. package/src/components/FieldHeader.tsx +0 -26
  233. package/src/components/InfoCollapsablePane.tsx +0 -90
  234. package/src/components/VariantInfoNestedTable.tsx +0 -127
  235. package/src/components/VariantSampleTable.tsx +0 -58
  236. package/src/components/VariantsSampleTable.tsx +0 -184
  237. package/src/components/VariantsTable.tsx +0 -125
  238. package/src/components/filter/FilterAllelicBalance.tsx +0 -81
  239. package/src/components/filter/FilterCategorical.tsx +0 -81
  240. package/src/components/filter/FilterClinVar.tsx +0 -21
  241. package/src/components/filter/FilterGene.tsx +0 -34
  242. package/src/components/filter/FilterHpo.tsx +0 -161
  243. package/src/components/filter/FilterInheritance.tsx +0 -162
  244. package/src/components/filter/FilterIntegerGq.tsx +0 -47
  245. package/src/components/filter/FilterVI.tsx +0 -68
  246. package/src/components/filter/FilterVariantType.tsx +0 -146
  247. package/src/components/filter/Filters.tsx +0 -29
  248. package/src/components/filter/InfoFilter.tsx +0 -39
  249. package/src/components/filter/InfoFilters.tsx +0 -35
  250. package/src/components/filter/SampleFilters.tsx +0 -93
  251. package/src/components/filter/SamplesFilters.tsx +0 -33
  252. package/src/components/record/Allele.tsx +0 -38
  253. package/src/components/record/AlleleBreakend.tsx +0 -5
  254. package/src/components/record/AlleleMissing.tsx +0 -5
  255. package/src/components/record/AlleleNucs.tsx +0 -49
  256. package/src/components/record/AlleleSymbolic.tsx +0 -5
  257. package/src/components/record/Alt.tsx +0 -17
  258. package/src/components/record/Chrom.tsx +0 -5
  259. package/src/components/record/Format.tsx +0 -40
  260. package/src/components/record/Info.tsx +0 -55
  261. package/src/components/record/Pos.tsx +0 -5
  262. package/src/components/record/Qual.tsx +0 -5
  263. package/src/components/record/RecordDownload.tsx +0 -66
  264. package/src/components/record/Ref.tsx +0 -6
  265. package/src/components/record/field/Field.tsx +0 -36
  266. package/src/components/record/field/FieldMultipleValue.tsx +0 -22
  267. package/src/components/record/field/FieldSingleValue.tsx +0 -35
  268. package/src/components/record/info/ClinVar.tsx +0 -81
  269. package/src/components/record/info/Consequence.tsx +0 -18
  270. package/src/components/record/info/Gene.tsx +0 -56
  271. package/src/components/record/info/GnomAD.tsx +0 -54
  272. package/src/components/record/info/Hpo.tsx +0 -52
  273. package/src/components/record/info/InheritanceModes.tsx +0 -22
  274. package/src/components/record/info/VipC.tsx +0 -23
  275. package/src/components/record/info/Vkgl.tsx +0 -42
  276. package/src/mocks/GRCh37/vcf/no_vep.vcf.blob +0 -61
  277. package/src/mocks/GRCh37/vcf/samples_0.vcf.blob +0 -93
  278. package/src/mocks/GRCh37/vcf/samples_1.vcf.blob +0 -93
  279. package/src/mocks/GRCh37/vcf/samples_100.vcf.blob +0 -93
  280. package/src/utils/ApiUtils.ts +0 -263
  281. package/src/utils/csqUtils.ts +0 -27
  282. package/src/utils/decisionTreeUtils.ts +0 -31
  283. package/src/utils/field.ts +0 -49
  284. package/src/utils/query.ts +0 -154
  285. package/src/utils/viewUtils.ts +0 -32
package/src/mocks/GRCh38/vcf/family.vcf.blob CHANGED
@@ -15,6 +15,7 @@
15
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  ##FORMAT=<ID=VIG,Number=.,Type=String,Description="Genes with an inheritance match.">
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  ##FORMAT=<ID=VIM,Number=1,Type=Integer,Description="Inheritance Match status.">
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  ##FORMAT=<ID=VIS,Number=.,Type=String,Description="An enumeration of possible sub inheritance modes like e.g. compound, non penetrance.">
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+ ##FORMAT=<ID=VIPC_S,Number=.,Type=String,Description="VIP decision tree classification.">
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  ##HPO=List of HPO terms for the gene
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  ##INFO=<ID=BND_DEPTH,Number=1,Type=Integer,Description="Read depth at local translocation breakend">
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  ##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|VIPC|VIPP|VIPL">
@@ -245,27 +246,27 @@
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  ##fileDate=20200320
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  ##reference=/vip/resources/GRCh38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz
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  #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Father MotherHasQuiteALongName Nephew Patient Sister Unrelated
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- chr1 9982480 . 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|||EntrezGene|||||0.04|0.08||pathogenic||1&1||||||||0|-36|-16|17|0.00|0.00|0.00|0.00|NMNAT1|VUS|0.16328752|||AR|LP||||chr1:9982480-9982480|3.94519e-05|0|P|filter&vkgl&exit_p|,T|downstream_gene_variant|MODIFIER|NMNAT1|64802|Transcript|NM_001297779.2|protein_coding||||||||||rs142968179&CM127756|1|714|1|||EntrezGene||||||||pathogenic||1&1||||||||0|-36|-16|17|0.00|0.00|0.00|0.00|NMNAT1|VUS|0.030009428|||AR|LP||||chr1:9982480-9982480|3.94519e-05|0|P|filter&vkgl&exit_p|,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||1|EntrezGene|||||0.04|0.08||pathogenic||1&1||||||||0|-36|-16|17|0.00|0.00|0.00|0.00|NMNAT1|VUS|0.16328752|||AR|LP||||chr1:9982480-9982480|3.94519e-05|0|P|filter&vkgl&exit_p| GT:DP:VI:VIC:VID:VIM:GQ 0|0:10:.:.:.:.:50 0|0:50:.:.:.:.:50 0|0:50:.:.:.:.:50 1|0:50:AD:.:1:0:50 0|0:50:.:.:.:.:50 0|0:50:.:.:.:.:50
249
- chr1 152548312 symbolic1 A <DEL> . PASS CSQ=deletion|transcript_ablation|HIGH|LCE3D|84648|Transcript|NM_032563.2|protein_coding|||||||||||1||-1||1|EntrezGene|||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,deletion|upstream_gene_variant|MODIFIER|LCE3C|353144|Transcript|NM_178434.3|protein_coding|||||||||||1|2608|1|||EntrezGene|||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,deletion|transcript_ablation|HIGH|LCE3E|353145|Transcript|NM_178435.4|protein_coding|||||||||||1||-1|||EntrezGene|||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000372937||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000013752||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000372939||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000372940||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001171682||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000254476||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000931036||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001171683||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00191731851||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00189591243||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00078414360||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00078058090||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00000257725||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|;SVLEN=-49314;SVTYPE=DEL GT:DP:VI:VIC:VID:VIM:VIS:GQ 0|0:10:.:.:.:.:.:50 0|0:50:.:.:.:.:.:50 0|0:50:.:.:.:.:.:50 1|0:50:AR,AD:chr4_105399137_G_A,chr7_41977712_C_,chr19_11105470_C_G,chr19_17341188_GA_G,chr9_104784352_AAAGAT_A,chr8_60852584_G_,chrM_15325_A_G,chr22_50189164_C_CTG,chr2_47408528_G_,chr20_63695639_C_T,chrX_49075362_A_T:1:0:AR_C:10 0|0:50:.:.:.:.:.:50 0|0:50:.:.:.:.:.:50
250
- chr2 47408528 symbolic2 G <INS> . PASS CSQ=insertion|splice_polypyrimidine_tract_variant&coding_sequence_variant&intron_variant&feature_elongation|LOW|MSH2|4436|Transcript|NM_000251.3|protein_coding|2-8/16|2-8/15|||376-?/3115|340-?/2805|114-?/934||||1||1||1|EntrezGene|||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|splice_polypyrimidine_tract_variant&coding_sequence_variant&intron_variant&feature_elongation|LOW|MSH2|4436|Transcript|NM_001258281.1|protein_coding|3-9/17|3-9/16|||281-?/3025|142-?/2607|48-?/868||||1||1|||EntrezGene|||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001031132||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000605106||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001031134||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000605107||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000605109||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001031136||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000605111||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00526224866||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00200869503||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00037157434||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00211420385||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00211397893||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00191281526||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00524206131||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00191128737||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00523779682||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00523716616||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00524736808||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00522488084||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00522348227||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00189912570||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00151154280||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00521803756||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00525714757||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00522888937||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00003947213||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00190965228||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00189989760||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00190028111||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00525662463||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00190489771||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00524615628||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00000366692||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00208026052||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|;SVLEN=-49314;SVTYPE=INS GT:DP:VI:VIC:VID:VIM:VIS:GQ 0|0:10:.:.:.:.:.:50 0|0:50:.:.:.:.:.:50 0|0:50:.:.:.:.:.:50 1|0:50:AR,AD:chr4_105399137_G_A,chr7_41977712_C_,chr19_11105470_C_G,chr19_17341188_GA_G,chr9_104784352_AAAGAT_A,chr8_60852584_G_,chrM_15325_A_G,chr22_50189164_C_CTG,chr1_152548312_A_,chr20_63695639_C_T,chrX_49075362_A_T:1:0:AR_C:50 0|0:50:.:.:.:.:.:50 0|0:50:.:.:.:.:.:50
251
- chr4 105399137 . 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|1||-1|||EntrezGene|||||0|0.985||pathogenic||1&1||||||||-34|27|-2|-43|0.00|0.00|0.00|0.00|PPA2|VUS|0.79802734|||AR|LP||||chr4:105399137-105399137|0.000434159|0|P|filter&vkgl&exit_p|,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|1||-1|||EntrezGene|||||0|0.992||pathogenic||1&1||||||||-34|27|-2|-43|0.00|0.00|0.00|0.00|PPA2|VUS|0.76154137|||AR|LP||||chr4:105399137-105399137|0.000434159|0|P|filter&vkgl&exit_p|,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|1||-1|||EntrezGene|||||0|0.995||pathogenic||1&1||||||||-34|27|-2|-43|0.00|0.00|0.00|0.00|PPA2|VUS|0.7596747|||AR|LP||||chr4:105399137-105399137|0.000434159|0|P|filter&vkgl&exit_p|,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|1||-1||1|EntrezGene|||||0|0.993||pathogenic||1&1||||||||-34|27|-2|-43|0.00|0.00|0.00|0.00|PPA2|VUS|0.7574089|||AR|LP||||chr4:105399137-105399137|0.000434159|0|P|filter&vkgl&exit_p|,A|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001252884|enhancer||||||||||rs138215926&CM1610192|1|||||||||||||pathogenic||1&1||||||||||||||||||||||||||chr4:105399137-105399137|0.000434159|0|P|filter&vkgl&clinVar&exit_p| GT:DP:VI:VIC:VID:VIG:VIM:VIS:GQ 0|0:10:.:.:.:.:.:.:50 0|0:50:.:.:.:.:.:.:50 0|0:50:.:.:.:.:.:.:50 1|0:50:AR,AD:chr7_41977712_C_,chr19_11105470_C_G,chr19_17341188_GA_G,chr8_60852584_G_,chrM_15325_A_G,chr22_50189164_C_CTG,chr1_152548312_A_,chr2_47408528_G_,chr20_63695639_C_T,chrX_49075362_A_T:1:27068:1:AR_C:50 0|0:50:.:.:.:.:.:.:50 0|0:50:.:.:.:.:.:.:50
252
- chr7 41977712 single_breakend_nation C C. . PASS CSQ=BND|coding_sequence_variant|MODIFIER|GLI3|2737|Transcript|NM_000168.6|protein_coding|12/15||||1938/8405|1657/4743|553/1580||||1||-1||1|EntrezGene|||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,BND|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000823237||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,BND|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000325885||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|;SVTYPE=BND GT:DP:VI:VIC:VID:VIM:VIS:GQ 0|0:10:.:.:.:.:.:50 0|0:50:.:.:.:.:.:50 0|0:50:.:.:.:.:.:50 1|0:50:AR,AD:chr4_105399137_G_A,chr19_11105470_C_G,chr19_17341188_GA_G,chr9_104784352_AAAGAT_A,chr8_60852584_G_,chr7_42025358_GACTC_G,chrM_15325_A_G,chr22_50189164_C_CTG,chr1_152548312_A_,chr2_47408528_G_,chr20_63695639_C_T,chrX_49075362_A_T:1:0:AR_C:50 0|0:50:.:.:.:.:.:50 0|0:50:.:.:.:.:.:50
253
- chr7 42025358 . GACTC G . PASS CSQ=-|frameshift_variant|HIGH|GLI3|2737|Transcript|NM_000168.6|protein_coding|9/15||NM_000168.6:c.1258_1261del|NP_000159.3:p.Glu420LeufsTer3|1539-1542/8405|1258-1261/4743|420-421/1580|ES/X|GAGTct/ct||1||-1||1|EntrezGene||||||||||||||||||18|21|-40|6|0.00|0.00|0.00|0.00|GLI3|VUS|0.98730624||1|AD|LP|||||||P|filter&vkgl&exit_p| GT:DP:VI:VIC:VID:VIG:VIM:VIS:GQ 0|0:10:.:.:.:.:.:.:50 0|0:50:.:.:.:.:.:.:50 0|0:50:.:.:.:.:.:.:50 1|0:50:AR,AD:chr7_41977712_C_:1:2737:1:AR_C:50 0|0:50:.:.:.:.:.:.:50 0|0:50:.:.:.:.:.:.:50
254
- chr8 60852584 breakend1 G ]11:134014225]G . PASS BND_DEPTH=26;CSQ=BND|intron_variant|MODIFIER|CHD7|55636|Transcript|NM_001316690.1|protein_coding||2/4|||||||||1||1|||EntrezGene|||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,BND|coding_sequence_variant|MODIFIER|CHD7|55636|Transcript|NM_017780.4|protein_coding|30/38||||6499/11606|5982/8994|1994/2997||||1||1||1|EntrezGene|||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,BND|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001138764||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|;MATEID=breakend2;MATE_BND_DEPTH=39;SVTYPE=BND GT:DP:VI:VIC:VID:VIM:VIS:GQ 0|0:10:.:.:.:.:.:50 0|0:50:.:.:.:.:.:50 0|0:50:.:.:.:.:.:50 1|0:50:AR,AD:chr4_105399137_G_A,chr7_41977712_C_,chr19_11105470_C_G,chr19_17341188_GA_G,chr9_104784352_AAAGAT_A,chrM_15325_A_G,chr22_50189164_C_CTG,chr1_152548312_A_,chr2_47408528_G_,chr20_63695639_C_T,chrX_49075362_A_T:1:0:AR_C:50 0|0:50:.:.:.:.:.:50 0|0:50:.:.:.:.:.:50
255
- chr8 144085597 . CAG C . PASS CSQ=-|frameshift_variant|HIGH|GPAA1|8733|Transcript|NM_003801.4|protein_coding|11/12||NM_003801.4:c.1477_1478del|NP_003792.1:p.Arg493GlyfsTer152|1574-1575/2054|1477-1478/1866|493/621|R/X|AGg/g|rs782339984|1||1||1|EntrezGene||||||||pathogenic||1||||||||-15|-8|12|-21|0.02|0.00|0.00|0.00|GPAA1|VUS|0.99313146|||AR|LP||||chr8:144085598-144085600|0.000144549|0|P|filter&vkgl&exit_p|,-|downstream_gene_variant|MODIFIER|EXOSC4|54512|Transcript|NM_019037.3|protein_coding||||||||||rs782339984|1|4950|1|||EntrezGene||||||||pathogenic||1||||||||-15|-8|12|-21|0.02|0.00|0.00|0.00|GPAA1|VUS|0.0936931||||||||chr8:144085598-144085600|0.000144549|0|P|filter&vkgl&clinVar&exit_p| GT:DP:VI:VIC:VID:VIM:GQ 0|0:10:.:.:.:.:50 0|0:50:.:.:.:.:50 0|0:50:.:.:.:.:50 1|0:50:AD:.:1:0:50 0|0:50:.:.:.:.:50 0|0:50:.:.:.:.:50
256
- chr9 104784352 . 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|0.983508|HP:0000951||AD&AR||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,-|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000889339|promoter_flanking_region|||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p| GT:DP:VI:VIC:VID:VIG:VIM:VIS:GQ 0|0:10:.:.:.:.:.:.:50 0|0:50:.:.:.:.:.:.:50 0|0:50:.:.:.:.:.:.:50 1|0:50:AR,AD:chr7_41977712_C_,chr19_11105470_C_G,chr19_17341188_GA_G,chr8_60852584_G_,chrM_15325_A_G,chr22_50189164_C_CTG,chr1_152548312_A_,chr2_47408528_G_,chr20_63695639_C_T,chrX_49075362_A_T:1:19:1:AR_C:50 0|0:50:.:.:.:.:.:.:50 0|0:50:.:.:.:.:.:.:50
257
- chr10 124402930 . 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|1||-1||1|EntrezGene||||||||likely_pathogenic&pathogenic||1&1|1737786&23076989&1609808&22674428|||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.98058724|||AR|LP||||chr10:124402930-124402930|2.6295e-05|0|P|filter&vkgl&exit_p|,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|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic||1&1|1737786&23076989&1609808&22674428|||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.9785161|||AR|LP||||chr10:124402930-124402930|2.6295e-05|0|P|filter&vkgl&exit_p|,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|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic||1&1|1737786&23076989&1609808&22674428|||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.98058724|||AR|LP||||chr10:124402930-124402930|2.6295e-05|0|P|filter&vkgl&exit_p|,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|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic||1&1|1737786&23076989&1609808&22674428|||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.9811948|||AR|LP||||chr10:124402930-124402930|2.6295e-05|0|P|filter&vkgl&exit_p|,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|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic||1&1|1737786&23076989&1609808&22674428|||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.9812247|||AR|LP||||chr10:124402930-124402930|2.6295e-05|0|P|filter&vkgl&exit_p|,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|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic||1&1|1737786&23076989&1609808&22674428|||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.9810348|||AR|LP||||chr10:124402930-124402930|2.6295e-05|0|P|filter&vkgl&exit_p|,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|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic||1&1|1737786&23076989&1609808&22674428|||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.98210436|||AR|LP||||chr10:124402930-124402930|2.6295e-05|0|P|filter&vkgl&exit_p|,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|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic||1&1|1737786&23076989&1609808&22674428|||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.9811948|||AR|LP||||chr10:124402930-124402930|2.6295e-05|0|P|filter&vkgl&exit_p|,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|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic||1&1|1737786&23076989&1609808&22674428|||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.9727213|||AR|LP||||chr10:124402930-124402930|2.6295e-05|0|P|filter&vkgl&exit_p|,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|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic||1&1|1737786&23076989&1609808&22674428|||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.974531|||AR|LP||||chr10:124402930-124402930|2.6295e-05|0|P|filter&vkgl&exit_p| GT:DP:VI:VIC:VID:VIM:GQ 0|0:10:.:.:.:.:50 0|0:50:.:.:.:.:50 0|0:50:.:.:.:.:50 1|0:50:AD:.:1:0:50 0|0:50:.:.:.:.:50 0|0:50:.:.:.:.:50
258
- chr11 134144330 breakend2 G G[8:61765143[ . PASS BND_DEPTH=39;CSQ=BND|intron_variant|MODIFIER|JAM3|83700|Transcript|NM_001205329.2|protein_coding||3/7|||||||||1||1|||EntrezGene|||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,BND|coding_sequence_variant|MODIFIER|JAM3|83700|Transcript|NM_032801.5|protein_coding|4/9||||359/3765|347/933|116/310||||1||1||1|EntrezGene|||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|;MATEID=breakend1;MATE_BND_DEPTH=26;SVTYPE=BND GT:DP:VI:VIC:VID:VIM:GQ 0|0:10:.:.:.:.:50 0|0:50:.:.:.:.:50 0|0:50:.:.:.:.:50 1|0:50:AD:.:1:0:50 0|0:50:.:.:.:.:50 0|0:50:.:.:.:.:50
259
- chr13 76995993 . 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|0.82795596|||AR|LP|||||||P|filter&vkgl&exit_p|,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|0.8734921|||AR|LP|||||||P|filter&vkgl&exit_p| GT:DP:VI:VIC:VID:VIM:GQ 0|0:10:.:.:.:.:50 0|0:50:.:.:.:.:50 0|0:50:.:.:.:.:50 1|0:50:AD:.:1:0:50 0|0:50:.:.:.:.:50 0|0:50:.:.:.:.:50
260
- chr14 88870063 . 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|||EntrezGene||||||||likely_pathogenic||1||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.9879852|HP:0000951||AR|LP|||||||P|filter&vkgl&exit_p|,-|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||||||||likely_pathogenic||1||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.985551|HP:0000951||AR|LP|||||||P|filter&vkgl&exit_p|,-|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||||||||likely_pathogenic||1||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.98350626|HP:0000951||AR|LP|||||||P|filter&vkgl&exit_p|,-|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||||||||likely_pathogenic||1||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.9825065|HP:0000951||AR|LP|||||||P|filter&vkgl&exit_p|,-|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||||||||likely_pathogenic||1||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.9880476|HP:0000951||AR|LP|||||||P|filter&vkgl&exit_p|,-|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||1|EntrezGene||||||||likely_pathogenic||1||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.97812086|HP:0000951||AR|LP|||||||P|filter&vkgl&exit_p|,-|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||||||||likely_pathogenic||1||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.9879701|HP:0000951||AR|LP|||||||P|filter&vkgl&exit_p|,-|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||||||||likely_pathogenic||1||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.98293847|HP:0000951||AR|LP|||||||P|filter&vkgl&exit_p|,-|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||||||||likely_pathogenic||1||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.20394427|HP:0000951||AR|LP|||||||P|filter&vkgl&exit_p| GT:DP:VI:VIC:VID:VIM:GQ 0|0:10:.:.:.:.:50 0|0:50:.:.:.:.:50 0|0:50:.:.:.:.:50 1|0:50:AD:.:1:0:50 0|0:50:.:.:.:.:50 0|0:50:.:.:.:.:50
261
- chr14 104701523 . 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|0.89743406|||AD|LP|||||||P|filter&vkgl&exit_p|,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|0.89743406|||AD|LP|||||||P|filter&vkgl&exit_p|,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|0.89743406|||AD|LP|||||||P|filter&vkgl&exit_p| GT:DP:VI:VIC:VID:VIG:VIM:GQ 0|0:10:.:.:.:.:.:50 0|0:50:.:.:.:.:.:50 0|0:50:.:.:.:.:.:50 1|0:50:AD:.:1:64423:1:50 0|0:50:.:.:.:.:.:50 0|0:50:.:.:.:.:.:50
262
- chr17 31229046 . 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|0.9921835|HP:0000951|1|AD|LP|||||||P|filter&vkgl&exit_p|,-|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|0.99201524|HP:0000951|1|AD|LP|||||||P|filter&vkgl&exit_p| GT:DP:VI:VIC:VID:VIG:VIM:VIS:GQ 0|0:10:.:.:.:.:.:.:50 0|0:50:.:.:.:.:.:.:50 0|0:50:.:.:.:.:.:.:50 1|0:9:AR,AD:chr17_31336861_T_G:1:4763:1:AR_C:50 0|0:50:.:.:.:.:.:.:50 0|0:50:.:.:.:.:.:.:50
263
- chr17 31336861 . 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|CM143458&CM141499|1||1|||EntrezGene|||||0|0.994||||1&1||||||||-42|41|-34|8|0.00|0.00|0.00|0.00|NF1|VUS|0.80934244|HP:0000951|1|AD|LP|||||||P|filter&vkgl&exit_p|,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|CM143458&CM141499|1||1||1|EntrezGene|||||0|0.993||||1&1||||||||-42|41|-34|8|0.00|0.00|0.00|0.00|NF1|VUS|0.80934244|HP:0000951|1|AD|LP|||||||P|filter&vkgl&exit_p| GT:DP:VI:VIC:VID:VIG:VIM:VIS:GQ 0|0:10:.:.:.:.:.:.:50 0|0:50:.:.:.:.:.:.:50 0|0:50:.:.:.:.:.:.:50 1|0:50:AR,AD:chr17_31229046_AC_A:1:4763:1:AR_C:50 0|0:50:.:.:.:.:.:.:50 0|0:50:.:.:.:.:.:.:50
264
- chr19 11105470 . C G . PASS CSQ=G|stop_gained|HIGH|LDLR|3949|Transcript|NM_000527.5|protein_coding|4/18||NM_000527.5:c.564C>G|NP_000518.1:p.Tyr188Ter|650/5173|564/2583|188/860|Y/*|taC/taG|rs121908034&CM920416|1||1||1|EntrezGene||||||||pathogenic/likely_pathogenic&pathogenic||1&1|25741868&27765764&17142622&20809525&8882879&1734722&10422803|||||||1|11|0|-14|0.00|0.00|0.00|0.00|LDLR|VUS|0.97251827|HP:0000951||AD&AR|LP|||||||P|filter&vkgl&exit_p|,G|stop_gained|HIGH|LDLR|3949|Transcript|NM_001195798.2|protein_coding|4/18||NM_001195798.2:c.564C>G|NP_001182727.1:p.Tyr188Ter|650/5167|564/2577|188/858|Y/*|taC/taG|rs121908034&CM920416|1||1|||EntrezGene||||||||pathogenic/likely_pathogenic&pathogenic||1&1|25741868&27765764&17142622&20809525&8882879&1734722&10422803|||||||1|11|0|-14|0.00|0.00|0.00|0.00|LDLR|VUS|0.97251827|HP:0000951||AD&AR|LP|||||||P|filter&vkgl&exit_p|,G|stop_gained|HIGH|LDLR|3949|Transcript|NM_001195799.2|protein_coding|3/17||NM_001195799.2:c.441C>G|NP_001182728.1:p.Tyr147Ter|527/5050|441/2460|147/819|Y/*|taC/taG|rs121908034&CM920416|1||1|||EntrezGene||||||||pathogenic/likely_pathogenic&pathogenic||1&1|25741868&27765764&17142622&20809525&8882879&1734722&10422803|||||||1|11|0|-14|0.00|0.00|0.00|0.00|LDLR|VUS|0.9850093|HP:0000951||AD&AR|LP|||||||P|filter&vkgl&exit_p|,G|intron_variant|MODIFIER|LDLR|3949|Transcript|NM_001195800.2|protein_coding||3/15|NM_001195800.2:c.314-1922C>G|||||||rs121908034&CM920416|1||1|||EntrezGene||||||||pathogenic/likely_pathogenic&pathogenic||1&1|25741868&27765764&17142622&20809525&8882879&1734722&10422803|||||||1|11|0|-14|0.00|0.00|0.00|0.00|LDLR|VUS|0.006388327|HP:0000951||AD&AR|LP|||||||P|filter&vkgl&exit_p|,G|intron_variant|MODIFIER|LDLR|3949|Transcript|NM_001195803.2|protein_coding||3/15|NM_001195803.2:c.314-1095C>G|||||||rs121908034&CM920416|1||1|||EntrezGene||||||||pathogenic/likely_pathogenic&pathogenic||1&1|25741868&27765764&17142622&20809525&8882879&1734722&10422803|||||||1|11|0|-14|0.00|0.00|0.00|0.00|LDLR|VUS|0.006388327|HP:0000951||AD&AR|LP|||||||P|filter&vkgl&exit_p|,G|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001219902|promoter_flanking_region||||||||||rs121908034&CM920416|1|||||||||||||pathogenic/likely_pathogenic&pathogenic||1&1|25741868&27765764&17142622&20809525&8882879&1734722&10422803||||||||||||||||||||||||||||P|filter&vkgl&clinVar&exit_p| GT:DP:VI:VIC:VID:VIG:VIM:VIS:GQ 0|0:10:.:.:.:.:.:.:50 0|0:50:.:.:.:.:.:.:50 0|0:50:.:.:.:.:.:.:50 1|0:50:AR,AD:chr4_105399137_G_A,chr7_41977712_C_,chr9_104784352_AAAGAT_A,chr8_60852584_G_,chr22_50189164_C_CTG,chr1_152548312_A_,chr2_47408528_G_,chr20_63695639_C_T,chrX_49075362_A_T:1:3949:1:AR_C:50 0|0:50:.:.:.:.:.:.:50 0|0:50:.:.:.:.:.:.:50
265
- chr19 17341188 . 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|0.9901776|HP:0000951||AR|LP|||||||P|filter&vkgl&exit_p|,-|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|0.9913974|HP:0000951||AR|LP|||||||P|filter&vkgl&exit_p|,-|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||1|EntrezGene|||||||1|||||||||||34|33|-7|33|0.01|0.00|0.00|0.00|GTPBP3|VUS|0.99110925|HP:0000951||AR|LP|||||||P|filter&vkgl&exit_p|,-|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|||EntrezGene|||||||1|||||||||||34|33|-7|33|0.01|0.00|0.00|0.00|GTPBP3|VUS|0.9916678|HP:0000951||AR|LP|||||||P|filter&vkgl&exit_p|,-|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000586166|promoter|||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,-|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001022836|CTCF_binding_site|||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,-|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00000278460||||||||||||1||1||||||||||||||||ENSPFM0305|8|N||HOXB2::ELF1||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p| GT:DP:VI:VIC:VID:VIG:VIM:VIS:GQ 0|0:10:.:.:.:.:.:.:50 0|0:50:.:.:.:.:.:.:50 0|0:50:.:.:.:.:.:.:50 1|0:50:AR,AD:chr4_105399137_G_A,chr7_41977712_C_,chr9_104784352_AAAGAT_A,chr8_60852584_G_,chr22_50189164_C_CTG,chr1_152548312_A_,chr2_47408528_G_,chr20_63695639_C_T,chrX_49075362_A_T:1:84705:1:AR_C:50 0|0:50:.:.:.:.:.:.:50 0|0:50:.:.:.:.:.:.:50
266
- chr20 63695639 . C T . PASS CSQ=T|downstream_gene_variant|MODIFIER|ARFRP1|10139|Transcript|NM_001134758.4|protein_coding||||||||||rs993254667|1|3008|-1|||EntrezGene|||||||||||||||||||||||||||VUS|0.017016819||||||||chr20:63695639-63695639|1.97117e-05|0|P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,T|downstream_gene_variant|MODIFIER|ARFRP1|10139|Transcript|NM_001267544.3|protein_coding||||||||||rs993254667|1|3008|-1|||EntrezGene|||||||||||||||||||||||||||VUS|0.017016819||||||||chr20:63695639-63695639|1.97117e-05|0|P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,T|downstream_gene_variant|MODIFIER|ARFRP1|10139|Transcript|NM_001267545.3|protein_coding||||||||||rs993254667|1|3008|-1|||EntrezGene|||||||||||||||||||||||||||VUS|0.017016819||||||||chr20:63695639-63695639|1.97117e-05|0|P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,T|downstream_gene_variant|MODIFIER|ARFRP1|10139|Transcript|NM_001267546.3|protein_coding||||||||||rs993254667|1|3008|-1|||EntrezGene|||||||||||||||||||||||||||VUS|0.017016819||||||||chr20:63695639-63695639|1.97117e-05|0|P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,T|downstream_gene_variant|MODIFIER|ARFRP1|10139|Transcript|NM_001267547.3|protein_coding||||||||||rs993254667|1|3008|-1|||EntrezGene|||||||||||||||||||||||||||VUS|0.017016819||||||||chr20:63695639-63695639|1.97117e-05|0|P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,T|downstream_gene_variant|MODIFIER|ARFRP1|10139|Transcript|NM_001267548.3|protein_coding||||||||||rs993254667|1|3008|-1|||EntrezGene|||||||||||||||||||||||||||VUS|0.017016819||||||||chr20:63695639-63695639|1.97117e-05|0|P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,T|downstream_gene_variant|MODIFIER|ARFRP1|10139|Transcript|NM_001267549.3|protein_coding||||||||||rs993254667|1|3008|-1|||EntrezGene|||||||||||||||||||||||||||VUS|0.017016819||||||||chr20:63695639-63695639|1.97117e-05|0|P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,T|missense_variant|MODERATE|RTEL1|51750|Transcript|NM_001283009.2|protein_coding|34/35||NM_001283009.2:c.3811C>T|NP_001269938.1:p.Arg1271Trp|4136/4615|3811/3903|1271/1300|R/W|Cgg/Tgg|rs993254667|1||1||1|EntrezGene|||||0.16|0.003||||||||||||12|-21|44|11|0.00|0.00|0.00|0.09|RTEL1|VUS|0.0055121304|HP:0000951||AD&AR|||||chr20:63695639-63695639|1.97117e-05|0|P|filter&vkgl&clinVar&gnomad&effect&sift&polyphen&exit_p|,T|intron_variant|MODIFIER|RTEL1|51750|Transcript|NM_001283010.1|protein_coding||33/33|NM_001283010.1:c.2984-139C>T|||||||rs993254667|1||1|||EntrezGene||||||||||||||||||12|-21|44|11|0.00|0.00|0.00|0.09|RTEL1|VUS|0.002660127|HP:0000951||AD&AR|||||chr20:63695639-63695639|1.97117e-05|0|P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,T|downstream_gene_variant|MODIFIER|ARFRP1|10139|Transcript|NM_003224.6|protein_coding||||||||||rs993254667|1|3008|-1|||EntrezGene|||||||||||||||||||||||||||VUS|0.017016819||||||||chr20:63695639-63695639|1.97117e-05|0|P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,T|upstream_gene_variant|MODIFIER|TNFRSF6B|8771|Transcript|NM_003823.4|protein_coding||||||||||rs993254667|1|1013|1|||EntrezGene|||||||||||||||||||||||||||VUS|0.0115982685||||||||chr20:63695639-63695639|1.97117e-05|0|P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,T|intron_variant|MODIFIER|RTEL1|51750|Transcript|NM_016434.4|protein_coding||34/34|NM_016434.4:c.3653-139C>T|||||||rs993254667|1||1|||EntrezGene||||||||||||||||||12|-21|44|11|0.00|0.00|0.00|0.09|RTEL1|VUS|0.002660127|HP:0000951||AD&AR|||||chr20:63695639-63695639|1.97117e-05|0|P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,T|intron_variant|MODIFIER|RTEL1|51750|Transcript|NM_032957.5|protein_coding||34/34|NM_032957.5:c.3725-139C>T|||||||rs993254667|1||1|||EntrezGene||||||||||||||||||12|-21|44|11|0.00|0.00|0.00|0.09|RTEL1|VUS|0.002660127|HP:0000951||AD&AR|||||chr20:63695639-63695639|1.97117e-05|0|P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,T|non_coding_transcript_exon_variant|MODIFIER|RTEL1-TNFRSF6B|100533107|Transcript|NR_037882.1|lncRNA|34/38||NR_037882.1:n.4638C>T||4638/5772|||||rs993254667|1||1|||EntrezGene||||||||||||||||||12|-21|44|11|0.00|0.00|0.00|0.09|RTEL1-TNFRSF6B|VUS|0.039789375||||||||chr20:63695639-63695639|1.97117e-05|0|P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,T|downstream_gene_variant|MODIFIER|ARFRP1|10139|Transcript|NR_051954.3|misc_RNA||||||||||rs993254667|1|3008|-1|||EntrezGene|||||||||||||||||||||||||||VUS|0.017016819||||||||chr20:63695639-63695639|1.97117e-05|0|P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,T|downstream_gene_variant|MODIFIER|ARFRP1|10139|Transcript|NR_051955.3|misc_RNA||||||||||rs993254667|1|3008|-1|||EntrezGene|||||||||||||||||||||||||||VUS|0.017016819||||||||chr20:63695639-63695639|1.97117e-05|0|P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,T|downstream_gene_variant|MODIFIER|ARFRP1|10139|Transcript|NR_051956.3|misc_RNA||||||||||rs993254667|1|3008|-1|||EntrezGene|||||||||||||||||||||||||||VUS|0.017016819||||||||chr20:63695639-63695639|1.97117e-05|0|P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,T|downstream_gene_variant|MODIFIER|ARFRP1|10139|Transcript|NR_051957.3|misc_RNA||||||||||rs993254667|1|3008|-1|||EntrezGene|||||||||||||||||||||||||||VUS|0.017016819||||||||chr20:63695639-63695639|1.97117e-05|0|P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,T|downstream_gene_variant|MODIFIER|ARFRP1|10139|Transcript|NR_051958.3|misc_RNA||||||||||rs993254667|1|3008|-1|||EntrezGene|||||||||||||||||||||||||||VUS|0.017016819||||||||chr20:63695639-63695639|1.97117e-05|0|P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,T|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000657794|CTCF_binding_site||||||||||rs993254667|1|||||||||||||||||||||||||||||||||||||||||chr20:63695639-63695639|1.97117e-05|0|P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p| GT:DP:VI:VIC:VID:VIG:VIM:VIS:GQ 0|0:10:.:.:.:.:.:.:50 0|0:50:.:.:.:.:.:.:50 0|0:50:.:.:.:.:.:.:50 1|0:50:AR,AD:chr4_105399137_G_A,chr7_41977712_C_,chr19_11105470_C_G,chr19_17341188_GA_G,chr9_104784352_AAAGAT_A,chr8_60852584_G_,chrM_15325_A_G,chr22_50189164_C_CTG,chr1_152548312_A_,chr2_47408528_G_:1:51750:1:AR_C:50 0|0:50:.:.:.:.:.:.:50 0|0:50:.:.:.:.:.:.:50
267
- chr22 50189164 . C CTG . PASS CSQ=TG|intron_variant|MODIFIER|TRABD|80305|Transcript|NM_001320484.2|protein_coding||1/9|NM_001320484.2:c.-35+3188_-35+3189insTG||||||||1||1|||EntrezGene|||||||||||||||||||||||||||VUS|0.014847702|||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,TG|intron_variant|MODIFIER|TRABD|80305|Transcript|NM_001320485.2|protein_coding||1/9|NM_001320485.2:c.-35+3188_-35+3189insTG||||||||1||1||1|EntrezGene|||||||||||||||||||||||||||VUS|0.014847702|||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,TG|upstream_gene_variant|MODIFIER|TRABD|80305|Transcript|NM_001320487.2|protein_coding|||||||||||1|1422|1|||EntrezGene|||||||||||||||||||||||||||VUS|0.25514466|||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,TG|upstream_gene_variant|MODIFIER|TRABD|80305|Transcript|NM_001320488.2|protein_coding|||||||||||1|1422|1|||EntrezGene|||||||||||||||||||||||||||VUS|0.25514466|||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,TG|intron_variant|MODIFIER|TRABD|80305|Transcript|NM_001378762.1|protein_coding||1/9|NM_001378762.1:c.-35+3119_-35+3120insTG||||||||1||1|||EntrezGene|||||||||||||||||||||||||||VUS|0.014847702|||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,TG|intron_variant|MODIFIER|TRABD|80305|Transcript|NM_001378765.1|protein_coding||1/10|NM_001378765.1:c.-35+3159_-35+3160insTG||||||||1||1|||EntrezGene|||||||||||||||||||||||||||VUS|0.014847702|||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,TG|intron_variant|MODIFIER|TRABD|80305|Transcript|NM_025204.4|protein_coding||1/9|NM_025204.4:c.-35+3163_-35+3164insTG||||||||1||1|||EntrezGene|||||||||||||||||||||||||||VUS|0.014847702|||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,TG|intron_variant&non_coding_transcript_variant|MODIFIER|TRABD|80305|Transcript|NR_135275.2|misc_RNA||1/9|NR_135275.2:n.64+3188_64+3189insTG||||||||1||1|||EntrezGene|||||||||||||||||||||||||||VUS|0.015001616|||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,TG|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000147690|promoter|||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p| GT:DP:VI:VIC:VID:VIM:VIS:GQ 0|0:10:.:.:.:.:.:50 0|0:50:.:.:.:.:.:50 0|0:50:.:.:.:.:.:50 1|0:50:AR,AD:chr4_105399137_G_A,chr7_41977712_C_,chr19_11105470_C_G,chr19_17341188_GA_G,chr9_104784352_AAAGAT_A,chr8_60852584_G_,chrM_15325_A_G,chr1_152548312_A_,chr2_47408528_G_,chr20_63695639_C_T,chrX_49075362_A_T:1:0:AR_C:50 0|0:50:.:.:.:.:.:50 0|0:50:.:.:.:.:.:50
268
- chr22 50283117 . 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|||EntrezGene||||||||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.15048689||||||||chr22:50283117-50283117|6.57263e-06|0|P|filter&vkgl&clinVar&gnomad&effect&sift&polyphen&impact&exit_p|,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|0.15048689||||||||chr22:50283117-50283117|6.57263e-06|0|P|filter&vkgl&clinVar&gnomad&effect&sift&polyphen&impact&exit_p|,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|0.94078785||||||||chr22:50283117-50283117|6.57263e-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|0.94078785||||||||chr22:50283117-50283117|6.57263e-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|0.94078785||||||||chr22:50283117-50283117|6.57263e-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|0.94078785||||||||chr22:50283117-50283117|6.57263e-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|0.94078785||||||||chr22:50283117-50283117|6.57263e-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|0.94078785||||||||chr22:50283117-50283117|6.57263e-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|0.94078785||||||||chr22:50283117-50283117|6.57263e-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|0.94078785||||||||chr22:50283117-50283117|6.57263e-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|0.94078785||||||||chr22:50283117-50283117|6.57263e-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|0.94078785||||||||chr22:50283117-50283117|6.57263e-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|0.94078785||||||||chr22:50283117-50283117|6.57263e-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|0.94078785||||||||chr22:50283117-50283117|6.57263e-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|0.94078785||||||||chr22:50283117-50283117|6.57263e-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|0.94078785||||||||chr22:50283117-50283117|6.57263e-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|0.94078785||||||||chr22:50283117-50283117|6.57263e-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|0.94078785||||||||chr22:50283117-50283117|6.57263e-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|0.94078785||||||||chr22:50283117-50283117|6.57263e-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|0.15048689||||||||chr22:50283117-50283117|6.57263e-06|0|P|filter&vkgl&clinVar&gnomad&effect&sift&polyphen&impact&exit_p|,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|0.15048689||||||||chr22:50283117-50283117|6.57263e-06|0|P|filter&vkgl&clinVar&gnomad&effect&sift&polyphen&impact&exit_p|,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|0.15048689||||||||chr22:50283117-50283117|6.57263e-06|0|P|filter&vkgl&clinVar&gnomad&effect&sift&polyphen&impact&exit_p|,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|0.15048689||||||||chr22:50283117-50283117|6.57263e-06|0|P|filter&vkgl&clinVar&gnomad&effect&sift&polyphen&impact&exit_p|,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||1|EntrezGene|||||0|1||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.94078785||||||||chr22:50283117-50283117|6.57263e-06|0|LP|filter&vkgl&clinVar&gnomad&effect&sift&exit_lp| GT:DP:VI:VIC:VID:VIM:GQ 0|0:10:.:.:.:.:50 0|0:50:.:.:.:.:50 0|0:50:.:.:.:.:50 1|0:50:AD:.:1:0 0|0:50:.:.:.:.:50 0|0:50:.:.:.:.:50
269
- chrX 49075362 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||1|EntrezGene||||||||||1||||||||27|28|-2|2|0.02|0.00|0.01|0.99|WDR45|VUS|0.98327905|HP:0000951||XL|LP|||||||P|filter&vkgl&exit_p|,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|||EntrezGene||||||||||1||||||||27|28|-2|2|0.02|0.00|0.01|0.99|WDR45|VUS|0.98327905|HP:0000951||XL|LP|||||||P|filter&vkgl&exit_p|,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|0.0113522755|||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&exit_p|,T|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000906841|CTCF_binding_site||||||||||CS135341|1|||||||||||||||1|||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p| GT:DP:VI:VIC:VID:VIG:VIM:VIS:GQ 0|0:10:.:.:.:.:.:.:50 0|0:50:.:.:.:.:.:.:50 0|0:50:.:.:.:.:.:.:50 1|0:50:XLD,XL,XLR:.:1:11152:1:XLD,XLR:50 0|0:50:.:.:.:.:.:.:50 0|0:50:.:.:.:.:.:.:50
270
- chrY 2787600 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|0.92795527|||||||||||P|filter&vkgl&clinVar&exit_p| GT:DP:VIC:VID:VIM:GQ 0:10:.:.:.:50 .:.:.:.:.:50 1:50:.:.:.:50 1:50:.:1:0:50 .:.:.:.:.:50 1:50:.:.:.:50
271
- chrM 15325 mt_chrom A G . PASS CSQ=G|intergenic_variant|MODIFIER|||||||||||||||rs1556424568|1||||1||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p| GT:DP:VIC:VID:VIM:GQ 0|0:10:.:.:.:50 0|0:50:.:.:.:50 0|0:50:.:.:.:50 1|0:50:.:1:0:50 0|0:50:.:.:.:50 0|0:50:.:.:.:50
249
+ chr1 9982480 . 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|||EntrezGene|||||0.04|0.08||pathogenic||1&1||||||||0|-36|-16|17|0.00|0.00|0.00|0.00|NMNAT1|VUS|0.16328752|||AR|LP||||chr1:9982480-9982480|3.94519e-05|0|P|filter&vkgl&exit_p|,T|downstream_gene_variant|MODIFIER|NMNAT1|64802|Transcript|NM_001297779.2|protein_coding||||||||||rs142968179&CM127756|1|714|1|||EntrezGene||||||||pathogenic||1&1||||||||0|-36|-16|17|0.00|0.00|0.00|0.00|NMNAT1|VUS|0.030009428|||AR|LP||||chr1:9982480-9982480|3.94519e-05|0|P|filter&vkgl&exit_p|,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||1|EntrezGene|||||0.04|0.08||pathogenic||1&1||||||||0|-36|-16|17|0.00|0.00|0.00|0.00|NMNAT1|VUS|0.16328752|||AR|LP||||chr1:9982480-9982480|3.94519e-05|0|P|filter&vkgl&exit_p| GT:DP:VI:VIC:VID:VIM:GQ:VIPC_S 0|0:10:.:.:.:.:50 0|0:50:.:.:.:.:50 0|0:50:.:.:.:.:50 1|0:50:AD:.:1:0:50:U1 0|0:50:.:.:.:.:50 0|0:50:.:.:.:.:50
250
+ chr1 152548312 symbolic1 A <DEL> . PASS CSQ=deletion|transcript_ablation|HIGH|LCE3D|84648|Transcript|NM_032563.2|protein_coding|||||||||||1||-1||1|EntrezGene|||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,deletion|upstream_gene_variant|MODIFIER|LCE3C|353144|Transcript|NM_178434.3|protein_coding|||||||||||1|2608|1|||EntrezGene|||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,deletion|transcript_ablation|HIGH|LCE3E|353145|Transcript|NM_178435.4|protein_coding|||||||||||1||-1|||EntrezGene|||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000372937||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000013752||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000372939||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000372940||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001171682||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000254476||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000931036||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001171683||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00191731851||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00189591243||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00078414360||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00078058090||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00000257725||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|;SVLEN=-49314;SVTYPE=DEL GT:DP:VI:VIC:VID:VIM:VIS:GQ:VIPC_S 0|0:10:.:.:.:.:.:50 0|0:50:.:.:.:.:.:50 0|0:50:.:.:.:.:.:50 1|0:50:AR,AD:chr4_105399137_G_A,chr7_41977712_C_,chr19_11105470_C_G,chr19_17341188_GA_G,chr9_104784352_AAAGAT_A,chr8_60852584_G_,chrM_15325_A_G,chr22_50189164_C_CTG,chr2_47408528_G_,chr20_63695639_C_T,chrX_49075362_A_T:1:0:AR_C:10:U1 0|0:50:.:.:.:.:.:50 0|0:50:.:.:.:.:.:50
251
+ chr2 47408528 symbolic2 G <INS> . PASS CSQ=insertion|splice_polypyrimidine_tract_variant&coding_sequence_variant&intron_variant&feature_elongation|LOW|MSH2|4436|Transcript|NM_000251.3|protein_coding|2-8/16|2-8/15|||376-?/3115|340-?/2805|114-?/934||||1||1||1|EntrezGene|||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|splice_polypyrimidine_tract_variant&coding_sequence_variant&intron_variant&feature_elongation|LOW|MSH2|4436|Transcript|NM_001258281.1|protein_coding|3-9/17|3-9/16|||281-?/3025|142-?/2607|48-?/868||||1||1|||EntrezGene|||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001031132||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000605106||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001031134||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000605107||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000605109||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001031136||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000605111||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00526224866||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00200869503||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00037157434||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00211420385||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00211397893||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00191281526||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00524206131||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00191128737||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00523779682||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00523716616||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00524736808||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00522488084||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00522348227||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00189912570||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00151154280||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00521803756||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00525714757||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00522888937||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00003947213||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00190965228||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00189989760||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00190028111||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00525662463||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00190489771||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00524615628||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00000366692||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00208026052||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|;SVLEN=-49314;SVTYPE=INS GT:DP:VI:VIC:VID:VIM:VIS:GQ:VIPC_S 0|0:10:.:.:.:.:.:50 0|0:50:.:.:.:.:.:50 0|0:50:.:.:.:.:.:50 1|0:50:AR,AD:chr4_105399137_G_A,chr7_41977712_C_,chr19_11105470_C_G,chr19_17341188_GA_G,chr9_104784352_AAAGAT_A,chr8_60852584_G_,chrM_15325_A_G,chr22_50189164_C_CTG,chr1_152548312_A_,chr20_63695639_C_T,chrX_49075362_A_T:1:0:AR_C:50:U1 0|0:50:.:.:.:.:.:50 0|0:50:.:.:.:.:.:50
252
+ chr4 105399137 . 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|1||-1|||EntrezGene|||||0|0.985||pathogenic||1&1||||||||-34|27|-2|-43|0.00|0.00|0.00|0.00|PPA2|VUS|0.79802734|||AR|LP||||chr4:105399137-105399137|0.000434159|0|P|filter&vkgl&exit_p|,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|1||-1|||EntrezGene|||||0|0.992||pathogenic||1&1||||||||-34|27|-2|-43|0.00|0.00|0.00|0.00|PPA2|VUS|0.76154137|||AR|LP||||chr4:105399137-105399137|0.000434159|0|P|filter&vkgl&exit_p|,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|1||-1|||EntrezGene|||||0|0.995||pathogenic||1&1||||||||-34|27|-2|-43|0.00|0.00|0.00|0.00|PPA2|VUS|0.7596747|||AR|LP||||chr4:105399137-105399137|0.000434159|0|P|filter&vkgl&exit_p|,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|1||-1||1|EntrezGene|||||0|0.993||pathogenic||1&1||||||||-34|27|-2|-43|0.00|0.00|0.00|0.00|PPA2|VUS|0.7574089|||AR|LP||||chr4:105399137-105399137|0.000434159|0|P|filter&vkgl&exit_p|,A|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001252884|enhancer||||||||||rs138215926&CM1610192|1|||||||||||||pathogenic||1&1||||||||||||||||||||||||||chr4:105399137-105399137|0.000434159|0|P|filter&vkgl&clinVar&exit_p| GT:DP:VI:VIC:VID:VIG:VIM:VIS:GQ:VIPC_S 0|0:10:.:.:.:.:.:.:50 0|0:50:.:.:.:.:.:.:50 0|0:50:.:.:.:.:.:.:50 1|0:50:AR,AD:chr7_41977712_C_,chr19_11105470_C_G,chr19_17341188_GA_G,chr8_60852584_G_,chrM_15325_A_G,chr22_50189164_C_CTG,chr1_152548312_A_,chr2_47408528_G_,chr20_63695639_C_T,chrX_49075362_A_T:1:27068:1:AR_C:50:U1 0|0:50:.:.:.:.:.:.:50 0|0:50:.:.:.:.:.:.:50
253
+ chr7 41977712 single_breakend_nation C C. . PASS CSQ=BND|coding_sequence_variant|MODIFIER|GLI3|2737|Transcript|NM_000168.6|protein_coding|12/15||||1938/8405|1657/4743|553/1580||||1||-1||1|EntrezGene|||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,BND|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000823237||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,BND|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000325885||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|;SVTYPE=BND GT:DP:VI:VIC:VID:VIM:VIS:GQ:VIPC_S 0|0:10:.:.:.:.:.:50 0|0:50:.:.:.:.:.:50 0|0:50:.:.:.:.:.:50 1|0:50:AR,AD:chr4_105399137_G_A,chr19_11105470_C_G,chr19_17341188_GA_G,chr9_104784352_AAAGAT_A,chr8_60852584_G_,chr7_42025358_GACTC_G,chrM_15325_A_G,chr22_50189164_C_CTG,chr1_152548312_A_,chr2_47408528_G_,chr20_63695639_C_T,chrX_49075362_A_T:1:0:AR_C:50:U1 0|0:50:.:.:.:.:.:50 0|0:50:.:.:.:.:.:50
254
+ chr7 42025358 . GACTC G . PASS CSQ=-|frameshift_variant|HIGH|GLI3|2737|Transcript|NM_000168.6|protein_coding|9/15||NM_000168.6:c.1258_1261del|NP_000159.3:p.Glu420LeufsTer3|1539-1542/8405|1258-1261/4743|420-421/1580|ES/X|GAGTct/ct||1||-1||1|EntrezGene||||||||||||||||||18|21|-40|6|0.00|0.00|0.00|0.00|GLI3|VUS|0.98730624||1|AD|LP|||||||P|filter&vkgl&exit_p| GT:DP:VI:VIC:VID:VIG:VIM:VIS:GQ:VIPC_S 0|0:10:.:.:.:.:.:.:50 0|0:50:.:.:.:.:.:.:50 0|0:50:.:.:.:.:.:.:50 1|0:50:AR,AD:chr7_41977712_C_:1:2737:1:AR_C:50:U1 0|0:50:.:.:.:.:.:.:50 0|0:50:.:.:.:.:.:.:50
255
+ chr8 60852584 breakend1 G ]11:134014225]G . PASS BND_DEPTH=26;CSQ=BND|intron_variant|MODIFIER|CHD7|55636|Transcript|NM_001316690.1|protein_coding||2/4|||||||||1||1|||EntrezGene|||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,BND|coding_sequence_variant|MODIFIER|CHD7|55636|Transcript|NM_017780.4|protein_coding|30/38||||6499/11606|5982/8994|1994/2997||||1||1||1|EntrezGene|||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,BND|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001138764||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|;MATEID=breakend2;MATE_BND_DEPTH=39;SVTYPE=BND GT:DP:VI:VIC:VID:VIM:VIS:GQ:VIPC_S 0|0:10:.:.:.:.:.:50 0|0:50:.:.:.:.:.:50 0|0:50:.:.:.:.:.:50 1|0:50:AR,AD:chr4_105399137_G_A,chr7_41977712_C_,chr19_11105470_C_G,chr19_17341188_GA_G,chr9_104784352_AAAGAT_A,chrM_15325_A_G,chr22_50189164_C_CTG,chr1_152548312_A_,chr2_47408528_G_,chr20_63695639_C_T,chrX_49075362_A_T:1:0:AR_C:50:U1 0|0:50:.:.:.:.:.:50 0|0:50:.:.:.:.:.:50
256
+ chr8 144085597 . CAG C . PASS CSQ=-|frameshift_variant|HIGH|GPAA1|8733|Transcript|NM_003801.4|protein_coding|11/12||NM_003801.4:c.1477_1478del|NP_003792.1:p.Arg493GlyfsTer152|1574-1575/2054|1477-1478/1866|493/621|R/X|AGg/g|rs782339984|1||1||1|EntrezGene||||||||pathogenic||1||||||||-15|-8|12|-21|0.02|0.00|0.00|0.00|GPAA1|VUS|0.99313146|||AR|LP||||chr8:144085598-144085600|0.000144549|0|P|filter&vkgl&exit_p|,-|downstream_gene_variant|MODIFIER|EXOSC4|54512|Transcript|NM_019037.3|protein_coding||||||||||rs782339984|1|4950|1|||EntrezGene||||||||pathogenic||1||||||||-15|-8|12|-21|0.02|0.00|0.00|0.00|GPAA1|VUS|0.0936931||||||||chr8:144085598-144085600|0.000144549|0|P|filter&vkgl&clinVar&exit_p| GT:DP:VI:VIC:VID:VIM:GQ:VIPC_S 0|0:10:.:.:.:.:50 0|0:50:.:.:.:.:50 0|0:50:.:.:.:.:50 1|0:50:AD:.:1:0:50:U1 0|0:50:.:.:.:.:50 0|0:50:.:.:.:.:50
257
+ chr9 104784352 . 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|0.983508|HP:0000951||AD&AR||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,-|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000889339|promoter_flanking_region|||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p| GT:DP:VI:VIC:VID:VIG:VIM:VIS:GQ:VIPC_S 0|0:10:.:.:.:.:.:.:50 0|0:50:.:.:.:.:.:.:50 0|0:50:.:.:.:.:.:.:50 1|0:50:AR,AD:chr7_41977712_C_,chr19_11105470_C_G,chr19_17341188_GA_G,chr8_60852584_G_,chrM_15325_A_G,chr22_50189164_C_CTG,chr1_152548312_A_,chr2_47408528_G_,chr20_63695639_C_T,chrX_49075362_A_T:1:19:1:AR_C:50:U1 0|0:50:.:.:.:.:.:.:50 0|0:50:.:.:.:.:.:.:50
258
+ chr10 124402930 . 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|1||-1||1|EntrezGene||||||||likely_pathogenic&pathogenic||1&1|1737786&23076989&1609808&22674428|||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.98058724|||AR|LP||||chr10:124402930-124402930|2.6295e-05|0|P|filter&vkgl&exit_p|,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|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic||1&1|1737786&23076989&1609808&22674428|||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.9785161|||AR|LP||||chr10:124402930-124402930|2.6295e-05|0|P|filter&vkgl&exit_p|,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|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic||1&1|1737786&23076989&1609808&22674428|||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.98058724|||AR|LP||||chr10:124402930-124402930|2.6295e-05|0|P|filter&vkgl&exit_p|,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|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic||1&1|1737786&23076989&1609808&22674428|||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.9811948|||AR|LP||||chr10:124402930-124402930|2.6295e-05|0|P|filter&vkgl&exit_p|,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|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic||1&1|1737786&23076989&1609808&22674428|||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.9812247|||AR|LP||||chr10:124402930-124402930|2.6295e-05|0|P|filter&vkgl&exit_p|,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|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic||1&1|1737786&23076989&1609808&22674428|||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.9810348|||AR|LP||||chr10:124402930-124402930|2.6295e-05|0|P|filter&vkgl&exit_p|,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|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic||1&1|1737786&23076989&1609808&22674428|||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.98210436|||AR|LP||||chr10:124402930-124402930|2.6295e-05|0|P|filter&vkgl&exit_p|,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|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic||1&1|1737786&23076989&1609808&22674428|||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.9811948|||AR|LP||||chr10:124402930-124402930|2.6295e-05|0|P|filter&vkgl&exit_p|,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|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic||1&1|1737786&23076989&1609808&22674428|||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.9727213|||AR|LP||||chr10:124402930-124402930|2.6295e-05|0|P|filter&vkgl&exit_p|,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|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic||1&1|1737786&23076989&1609808&22674428|||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.974531|||AR|LP||||chr10:124402930-124402930|2.6295e-05|0|P|filter&vkgl&exit_p| GT:DP:VI:VIC:VID:VIM:GQ:VIPC_S 0|0:10:.:.:.:.:50 0|0:50:.:.:.:.:50 0|0:50:.:.:.:.:50 1|0:50:AD:.:1:0:50:U1 0|0:50:.:.:.:.:50 0|0:50:.:.:.:.:50
259
+ chr11 134144330 breakend2 G G[8:61765143[ . PASS BND_DEPTH=39;CSQ=BND|intron_variant|MODIFIER|JAM3|83700|Transcript|NM_001205329.2|protein_coding||3/7|||||||||1||1|||EntrezGene|||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,BND|coding_sequence_variant|MODIFIER|JAM3|83700|Transcript|NM_032801.5|protein_coding|4/9||||359/3765|347/933|116/310||||1||1||1|EntrezGene|||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|;MATEID=breakend1;MATE_BND_DEPTH=26;SVTYPE=BND GT:DP:VI:VIC:VID:VIM:GQ:VIPC_S 0|0:10:.:.:.:.:50 0|0:50:.:.:.:.:50 0|0:50:.:.:.:.:50 1|0:50:AD:.:1:0:50:U1 0|0:50:.:.:.:.:50 0|0:50:.:.:.:.:50
260
+ chr13 76995993 . 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|0.82795596|||AR|LP|||||||P|filter&vkgl&exit_p|,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|0.8734921|||AR|LP|||||||P|filter&vkgl&exit_p| GT:DP:VI:VIC:VID:VIM:GQ:VIPC_S 0|0:10:.:.:.:.:50 0|0:50:.:.:.:.:50 0|0:50:.:.:.:.:50 1|0:50:AD:.:1:0:50:U1 0|0:50:.:.:.:.:50 0|0:50:.:.:.:.:50
261
+ chr14 88870063 . 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|||EntrezGene||||||||likely_pathogenic||1||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.9879852|HP:0000951||AR|LP|||||||P|filter&vkgl&exit_p|,-|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||||||||likely_pathogenic||1||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.985551|HP:0000951||AR|LP|||||||P|filter&vkgl&exit_p|,-|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||||||||likely_pathogenic||1||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.98350626|HP:0000951||AR|LP|||||||P|filter&vkgl&exit_p|,-|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||||||||likely_pathogenic||1||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.9825065|HP:0000951||AR|LP|||||||P|filter&vkgl&exit_p|,-|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||||||||likely_pathogenic||1||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.9880476|HP:0000951||AR|LP|||||||P|filter&vkgl&exit_p|,-|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||1|EntrezGene||||||||likely_pathogenic||1||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.97812086|HP:0000951||AR|LP|||||||P|filter&vkgl&exit_p|,-|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||||||||likely_pathogenic||1||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.9879701|HP:0000951||AR|LP|||||||P|filter&vkgl&exit_p|,-|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||||||||likely_pathogenic||1||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.98293847|HP:0000951||AR|LP|||||||P|filter&vkgl&exit_p|,-|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||||||||likely_pathogenic||1||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.20394427|HP:0000951||AR|LP|||||||P|filter&vkgl&exit_p| GT:DP:VI:VIC:VID:VIM:GQ:VIPC_S 0|0:10:.:.:.:.:50 0|0:50:.:.:.:.:50 0|0:50:.:.:.:.:50 1|0:50:AD:.:1:0:50:U1 0|0:50:.:.:.:.:50 0|0:50:.:.:.:.:50
262
+ chr14 104701523 . 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|0.89743406|||AD|LP|||||||P|filter&vkgl&exit_p|,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|0.89743406|||AD|LP|||||||P|filter&vkgl&exit_p|,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|0.89743406|||AD|LP|||||||P|filter&vkgl&exit_p| GT:DP:VI:VIC:VID:VIG:VIM:GQ:VIPC_S 0|0:10:.:.:.:.:.:50 0|0:50:.:.:.:.:.:50 0|0:50:.:.:.:.:.:50 1|0:50:AD:.:1:64423:1:50:U1 0|0:50:.:.:.:.:.:50 0|0:50:.:.:.:.:.:50
263
+ chr17 31229046 . 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|0.9921835|HP:0000951|1|AD|LP|||||||P|filter&vkgl&exit_p|,-|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|0.99201524|HP:0000951|1|AD|LP|||||||P|filter&vkgl&exit_p| GT:DP:VI:VIC:VID:VIG:VIM:VIS:GQ:VIPC_S 0|0:10:.:.:.:.:.:.:50 0|0:50:.:.:.:.:.:.:50 0|0:50:.:.:.:.:.:.:50 1|0:9:AR,AD:chr17_31336861_T_G:1:4763:1:AR_C:50:U1 0|0:50:.:.:.:.:.:.:50 0|0:50:.:.:.:.:.:.:50
264
+ chr17 31336861 . 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|CM143458&CM141499|1||1|||EntrezGene|||||0|0.994||||1&1||||||||-42|41|-34|8|0.00|0.00|0.00|0.00|NF1|VUS|0.80934244|HP:0000951|1|AD|LP|||||||P|filter&vkgl&exit_p|,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|CM143458&CM141499|1||1||1|EntrezGene|||||0|0.993||||1&1||||||||-42|41|-34|8|0.00|0.00|0.00|0.00|NF1|VUS|0.80934244|HP:0000951|1|AD|LP|||||||P|filter&vkgl&exit_p| GT:DP:VI:VIC:VID:VIG:VIM:VIS:GQ:VIPC_S 0|0:10:.:.:.:.:.:.:50 0|0:50:.:.:.:.:.:.:50 0|0:50:.:.:.:.:.:.:50 1|0:50:AR,AD:chr17_31229046_AC_A:1:4763:1:AR_C:50:U1 0|0:50:.:.:.:.:.:.:50 0|0:50:.:.:.:.:.:.:50
265
+ chr19 11105470 . C G . PASS CSQ=G|stop_gained|HIGH|LDLR|3949|Transcript|NM_000527.5|protein_coding|4/18||NM_000527.5:c.564C>G|NP_000518.1:p.Tyr188Ter|650/5173|564/2583|188/860|Y/*|taC/taG|rs121908034&CM920416|1||1||1|EntrezGene||||||||pathogenic/likely_pathogenic&pathogenic||1&1|25741868&27765764&17142622&20809525&8882879&1734722&10422803|||||||1|11|0|-14|0.00|0.00|0.00|0.00|LDLR|VUS|0.97251827|HP:0000951||AD&AR|LP|||||||P|filter&vkgl&exit_p|,G|stop_gained|HIGH|LDLR|3949|Transcript|NM_001195798.2|protein_coding|4/18||NM_001195798.2:c.564C>G|NP_001182727.1:p.Tyr188Ter|650/5167|564/2577|188/858|Y/*|taC/taG|rs121908034&CM920416|1||1|||EntrezGene||||||||pathogenic/likely_pathogenic&pathogenic||1&1|25741868&27765764&17142622&20809525&8882879&1734722&10422803|||||||1|11|0|-14|0.00|0.00|0.00|0.00|LDLR|VUS|0.97251827|HP:0000951||AD&AR|LP|||||||P|filter&vkgl&exit_p|,G|stop_gained|HIGH|LDLR|3949|Transcript|NM_001195799.2|protein_coding|3/17||NM_001195799.2:c.441C>G|NP_001182728.1:p.Tyr147Ter|527/5050|441/2460|147/819|Y/*|taC/taG|rs121908034&CM920416|1||1|||EntrezGene||||||||pathogenic/likely_pathogenic&pathogenic||1&1|25741868&27765764&17142622&20809525&8882879&1734722&10422803|||||||1|11|0|-14|0.00|0.00|0.00|0.00|LDLR|VUS|0.9850093|HP:0000951||AD&AR|LP|||||||P|filter&vkgl&exit_p|,G|intron_variant|MODIFIER|LDLR|3949|Transcript|NM_001195800.2|protein_coding||3/15|NM_001195800.2:c.314-1922C>G|||||||rs121908034&CM920416|1||1|||EntrezGene||||||||pathogenic/likely_pathogenic&pathogenic||1&1|25741868&27765764&17142622&20809525&8882879&1734722&10422803|||||||1|11|0|-14|0.00|0.00|0.00|0.00|LDLR|VUS|0.006388327|HP:0000951||AD&AR|LP|||||||P|filter&vkgl&exit_p|,G|intron_variant|MODIFIER|LDLR|3949|Transcript|NM_001195803.2|protein_coding||3/15|NM_001195803.2:c.314-1095C>G|||||||rs121908034&CM920416|1||1|||EntrezGene||||||||pathogenic/likely_pathogenic&pathogenic||1&1|25741868&27765764&17142622&20809525&8882879&1734722&10422803|||||||1|11|0|-14|0.00|0.00|0.00|0.00|LDLR|VUS|0.006388327|HP:0000951||AD&AR|LP|||||||P|filter&vkgl&exit_p|,G|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001219902|promoter_flanking_region||||||||||rs121908034&CM920416|1|||||||||||||pathogenic/likely_pathogenic&pathogenic||1&1|25741868&27765764&17142622&20809525&8882879&1734722&10422803||||||||||||||||||||||||||||P|filter&vkgl&clinVar&exit_p| GT:DP:VI:VIC:VID:VIG:VIM:VIS:GQ:VIPC_S 0|0:10:.:.:.:.:.:.:50 0|0:50:.:.:.:.:.:.:50 0|0:50:.:.:.:.:.:.:50 1|0:50:AR,AD:chr4_105399137_G_A,chr7_41977712_C_,chr9_104784352_AAAGAT_A,chr8_60852584_G_,chr22_50189164_C_CTG,chr1_152548312_A_,chr2_47408528_G_,chr20_63695639_C_T,chrX_49075362_A_T:1:3949:1:AR_C:50:U1 0|0:50:.:.:.:.:.:.:50 0|0:50:.:.:.:.:.:.:50
266
+ chr19 17341188 . 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|0.9901776|HP:0000951||AR|LP|||||||P|filter&vkgl&exit_p|,-|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|0.9913974|HP:0000951||AR|LP|||||||P|filter&vkgl&exit_p|,-|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||1|EntrezGene|||||||1|||||||||||34|33|-7|33|0.01|0.00|0.00|0.00|GTPBP3|VUS|0.99110925|HP:0000951||AR|LP|||||||P|filter&vkgl&exit_p|,-|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|||EntrezGene|||||||1|||||||||||34|33|-7|33|0.01|0.00|0.00|0.00|GTPBP3|VUS|0.9916678|HP:0000951||AR|LP|||||||P|filter&vkgl&exit_p|,-|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000586166|promoter|||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,-|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001022836|CTCF_binding_site|||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,-|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00000278460||||||||||||1||1||||||||||||||||ENSPFM0305|8|N||HOXB2::ELF1||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p| GT:DP:VI:VIC:VID:VIG:VIM:VIS:GQ:VIPC_S 0|0:10:.:.:.:.:.:.:50 0|0:50:.:.:.:.:.:.:50 0|0:50:.:.:.:.:.:.:50 1|0:50:AR,AD:chr4_105399137_G_A,chr7_41977712_C_,chr9_104784352_AAAGAT_A,chr8_60852584_G_,chr22_50189164_C_CTG,chr1_152548312_A_,chr2_47408528_G_,chr20_63695639_C_T,chrX_49075362_A_T:1:84705:1:AR_C:50:U1 0|0:50:.:.:.:.:.:.:50 0|0:50:.:.:.:.:.:.:50
267
+ chr20 63695639 . C T . PASS CSQ=T|downstream_gene_variant|MODIFIER|ARFRP1|10139|Transcript|NM_001134758.4|protein_coding||||||||||rs993254667|1|3008|-1|||EntrezGene|||||||||||||||||||||||||||VUS|0.017016819||||||||chr20:63695639-63695639|1.97117e-05|0|P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,T|downstream_gene_variant|MODIFIER|ARFRP1|10139|Transcript|NM_001267544.3|protein_coding||||||||||rs993254667|1|3008|-1|||EntrezGene|||||||||||||||||||||||||||VUS|0.017016819||||||||chr20:63695639-63695639|1.97117e-05|0|P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,T|downstream_gene_variant|MODIFIER|ARFRP1|10139|Transcript|NM_001267545.3|protein_coding||||||||||rs993254667|1|3008|-1|||EntrezGene|||||||||||||||||||||||||||VUS|0.017016819||||||||chr20:63695639-63695639|1.97117e-05|0|P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,T|downstream_gene_variant|MODIFIER|ARFRP1|10139|Transcript|NM_001267546.3|protein_coding||||||||||rs993254667|1|3008|-1|||EntrezGene|||||||||||||||||||||||||||VUS|0.017016819||||||||chr20:63695639-63695639|1.97117e-05|0|P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,T|downstream_gene_variant|MODIFIER|ARFRP1|10139|Transcript|NM_001267547.3|protein_coding||||||||||rs993254667|1|3008|-1|||EntrezGene|||||||||||||||||||||||||||VUS|0.017016819||||||||chr20:63695639-63695639|1.97117e-05|0|P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,T|downstream_gene_variant|MODIFIER|ARFRP1|10139|Transcript|NM_001267548.3|protein_coding||||||||||rs993254667|1|3008|-1|||EntrezGene|||||||||||||||||||||||||||VUS|0.017016819||||||||chr20:63695639-63695639|1.97117e-05|0|P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,T|downstream_gene_variant|MODIFIER|ARFRP1|10139|Transcript|NM_001267549.3|protein_coding||||||||||rs993254667|1|3008|-1|||EntrezGene|||||||||||||||||||||||||||VUS|0.017016819||||||||chr20:63695639-63695639|1.97117e-05|0|P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,T|missense_variant|MODERATE|RTEL1|51750|Transcript|NM_001283009.2|protein_coding|34/35||NM_001283009.2:c.3811C>T|NP_001269938.1:p.Arg1271Trp|4136/4615|3811/3903|1271/1300|R/W|Cgg/Tgg|rs993254667|1||1||1|EntrezGene|||||0.16|0.003||||||||||||12|-21|44|11|0.00|0.00|0.00|0.09|RTEL1|VUS|0.0055121304|HP:0000951||AD&AR|||||chr20:63695639-63695639|1.97117e-05|0|P|filter&vkgl&clinVar&gnomad&effect&sift&polyphen&exit_p|,T|intron_variant|MODIFIER|RTEL1|51750|Transcript|NM_001283010.1|protein_coding||33/33|NM_001283010.1:c.2984-139C>T|||||||rs993254667|1||1|||EntrezGene||||||||||||||||||12|-21|44|11|0.00|0.00|0.00|0.09|RTEL1|VUS|0.002660127|HP:0000951||AD&AR|||||chr20:63695639-63695639|1.97117e-05|0|P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,T|downstream_gene_variant|MODIFIER|ARFRP1|10139|Transcript|NM_003224.6|protein_coding||||||||||rs993254667|1|3008|-1|||EntrezGene|||||||||||||||||||||||||||VUS|0.017016819||||||||chr20:63695639-63695639|1.97117e-05|0|P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,T|upstream_gene_variant|MODIFIER|TNFRSF6B|8771|Transcript|NM_003823.4|protein_coding||||||||||rs993254667|1|1013|1|||EntrezGene|||||||||||||||||||||||||||VUS|0.0115982685||||||||chr20:63695639-63695639|1.97117e-05|0|P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,T|intron_variant|MODIFIER|RTEL1|51750|Transcript|NM_016434.4|protein_coding||34/34|NM_016434.4:c.3653-139C>T|||||||rs993254667|1||1|||EntrezGene||||||||||||||||||12|-21|44|11|0.00|0.00|0.00|0.09|RTEL1|VUS|0.002660127|HP:0000951||AD&AR|||||chr20:63695639-63695639|1.97117e-05|0|P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,T|intron_variant|MODIFIER|RTEL1|51750|Transcript|NM_032957.5|protein_coding||34/34|NM_032957.5:c.3725-139C>T|||||||rs993254667|1||1|||EntrezGene||||||||||||||||||12|-21|44|11|0.00|0.00|0.00|0.09|RTEL1|VUS|0.002660127|HP:0000951||AD&AR|||||chr20:63695639-63695639|1.97117e-05|0|P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,T|non_coding_transcript_exon_variant|MODIFIER|RTEL1-TNFRSF6B|100533107|Transcript|NR_037882.1|lncRNA|34/38||NR_037882.1:n.4638C>T||4638/5772|||||rs993254667|1||1|||EntrezGene||||||||||||||||||12|-21|44|11|0.00|0.00|0.00|0.09|RTEL1-TNFRSF6B|VUS|0.039789375||||||||chr20:63695639-63695639|1.97117e-05|0|P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,T|downstream_gene_variant|MODIFIER|ARFRP1|10139|Transcript|NR_051954.3|misc_RNA||||||||||rs993254667|1|3008|-1|||EntrezGene|||||||||||||||||||||||||||VUS|0.017016819||||||||chr20:63695639-63695639|1.97117e-05|0|P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,T|downstream_gene_variant|MODIFIER|ARFRP1|10139|Transcript|NR_051955.3|misc_RNA||||||||||rs993254667|1|3008|-1|||EntrezGene|||||||||||||||||||||||||||VUS|0.017016819||||||||chr20:63695639-63695639|1.97117e-05|0|P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,T|downstream_gene_variant|MODIFIER|ARFRP1|10139|Transcript|NR_051956.3|misc_RNA||||||||||rs993254667|1|3008|-1|||EntrezGene|||||||||||||||||||||||||||VUS|0.017016819||||||||chr20:63695639-63695639|1.97117e-05|0|P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,T|downstream_gene_variant|MODIFIER|ARFRP1|10139|Transcript|NR_051957.3|misc_RNA||||||||||rs993254667|1|3008|-1|||EntrezGene|||||||||||||||||||||||||||VUS|0.017016819||||||||chr20:63695639-63695639|1.97117e-05|0|P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,T|downstream_gene_variant|MODIFIER|ARFRP1|10139|Transcript|NR_051958.3|misc_RNA||||||||||rs993254667|1|3008|-1|||EntrezGene|||||||||||||||||||||||||||VUS|0.017016819||||||||chr20:63695639-63695639|1.97117e-05|0|P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,T|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000657794|CTCF_binding_site||||||||||rs993254667|1|||||||||||||||||||||||||||||||||||||||||chr20:63695639-63695639|1.97117e-05|0|P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p| GT:DP:VI:VIC:VID:VIG:VIM:VIS:GQ:VIPC_S 0|0:10:.:.:.:.:.:.:50 0|0:50:.:.:.:.:.:.:50 0|0:50:.:.:.:.:.:.:50 1|0:50:AR,AD:chr4_105399137_G_A,chr7_41977712_C_,chr19_11105470_C_G,chr19_17341188_GA_G,chr9_104784352_AAAGAT_A,chr8_60852584_G_,chrM_15325_A_G,chr22_50189164_C_CTG,chr1_152548312_A_,chr2_47408528_G_:1:51750:1:AR_C:50:U1 0|0:50:.:.:.:.:.:.:50 0|0:50:.:.:.:.:.:.:50
268
+ chr22 50189164 . C CTG . PASS CSQ=TG|intron_variant|MODIFIER|TRABD|80305|Transcript|NM_001320484.2|protein_coding||1/9|NM_001320484.2:c.-35+3188_-35+3189insTG||||||||1||1|||EntrezGene|||||||||||||||||||||||||||VUS|0.014847702|||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,TG|intron_variant|MODIFIER|TRABD|80305|Transcript|NM_001320485.2|protein_coding||1/9|NM_001320485.2:c.-35+3188_-35+3189insTG||||||||1||1||1|EntrezGene|||||||||||||||||||||||||||VUS|0.014847702|||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,TG|upstream_gene_variant|MODIFIER|TRABD|80305|Transcript|NM_001320487.2|protein_coding|||||||||||1|1422|1|||EntrezGene|||||||||||||||||||||||||||VUS|0.25514466|||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,TG|upstream_gene_variant|MODIFIER|TRABD|80305|Transcript|NM_001320488.2|protein_coding|||||||||||1|1422|1|||EntrezGene|||||||||||||||||||||||||||VUS|0.25514466|||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,TG|intron_variant|MODIFIER|TRABD|80305|Transcript|NM_001378762.1|protein_coding||1/9|NM_001378762.1:c.-35+3119_-35+3120insTG||||||||1||1|||EntrezGene|||||||||||||||||||||||||||VUS|0.014847702|||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,TG|intron_variant|MODIFIER|TRABD|80305|Transcript|NM_001378765.1|protein_coding||1/10|NM_001378765.1:c.-35+3159_-35+3160insTG||||||||1||1|||EntrezGene|||||||||||||||||||||||||||VUS|0.014847702|||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,TG|intron_variant|MODIFIER|TRABD|80305|Transcript|NM_025204.4|protein_coding||1/9|NM_025204.4:c.-35+3163_-35+3164insTG||||||||1||1|||EntrezGene|||||||||||||||||||||||||||VUS|0.014847702|||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,TG|intron_variant&non_coding_transcript_variant|MODIFIER|TRABD|80305|Transcript|NR_135275.2|misc_RNA||1/9|NR_135275.2:n.64+3188_64+3189insTG||||||||1||1|||EntrezGene|||||||||||||||||||||||||||VUS|0.015001616|||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,TG|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000147690|promoter|||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p| GT:DP:VI:VIC:VID:VIM:VIS:GQ:VIPC_S 0|0:10:.:.:.:.:.:50 0|0:50:.:.:.:.:.:50 0|0:50:.:.:.:.:.:50 1|0:50:AR,AD:chr4_105399137_G_A,chr7_41977712_C_,chr19_11105470_C_G,chr19_17341188_GA_G,chr9_104784352_AAAGAT_A,chr8_60852584_G_,chrM_15325_A_G,chr1_152548312_A_,chr2_47408528_G_,chr20_63695639_C_T,chrX_49075362_A_T:1:0:AR_C:50:U1 0|0:50:.:.:.:.:.:50 0|0:50:.:.:.:.:.:50
269
+ chr22 50283117 . 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|||EntrezGene||||||||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.15048689||||||||chr22:50283117-50283117|6.57263e-06|0|P|filter&vkgl&clinVar&gnomad&effect&sift&polyphen&impact&exit_p|,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|0.15048689||||||||chr22:50283117-50283117|6.57263e-06|0|P|filter&vkgl&clinVar&gnomad&effect&sift&polyphen&impact&exit_p|,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|0.94078785||||||||chr22:50283117-50283117|6.57263e-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|0.94078785||||||||chr22:50283117-50283117|6.57263e-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|0.94078785||||||||chr22:50283117-50283117|6.57263e-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|0.94078785||||||||chr22:50283117-50283117|6.57263e-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|0.94078785||||||||chr22:50283117-50283117|6.57263e-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|0.94078785||||||||chr22:50283117-50283117|6.57263e-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|0.94078785||||||||chr22:50283117-50283117|6.57263e-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|0.94078785||||||||chr22:50283117-50283117|6.57263e-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|0.94078785||||||||chr22:50283117-50283117|6.57263e-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|0.94078785||||||||chr22:50283117-50283117|6.57263e-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|0.94078785||||||||chr22:50283117-50283117|6.57263e-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|0.94078785||||||||chr22:50283117-50283117|6.57263e-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|0.94078785||||||||chr22:50283117-50283117|6.57263e-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|0.94078785||||||||chr22:50283117-50283117|6.57263e-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|0.94078785||||||||chr22:50283117-50283117|6.57263e-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|0.94078785||||||||chr22:50283117-50283117|6.57263e-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|0.94078785||||||||chr22:50283117-50283117|6.57263e-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|0.15048689||||||||chr22:50283117-50283117|6.57263e-06|0|P|filter&vkgl&clinVar&gnomad&effect&sift&polyphen&impact&exit_p|,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|0.15048689||||||||chr22:50283117-50283117|6.57263e-06|0|P|filter&vkgl&clinVar&gnomad&effect&sift&polyphen&impact&exit_p|,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|0.15048689||||||||chr22:50283117-50283117|6.57263e-06|0|P|filter&vkgl&clinVar&gnomad&effect&sift&polyphen&impact&exit_p|,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|0.15048689||||||||chr22:50283117-50283117|6.57263e-06|0|P|filter&vkgl&clinVar&gnomad&effect&sift&polyphen&impact&exit_p|,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||1|EntrezGene|||||0|1||||||||||||-2|36|-32|-38|0.05|0.00|0.00|0.00|PLXNB2|VUS|0.94078785||||||||chr22:50283117-50283117|6.57263e-06|0|LP|filter&vkgl&clinVar&gnomad&effect&sift&exit_lp| GT:DP:VI:VIC:VID:VIM:GQ:VIPC_S 0|0:10:.:.:.:.:50 0|0:50:.:.:.:.:50 0|0:50:.:.:.:.:50 1|0:50:AD:.:1:0:50:U1 0|0:50:.:.:.:.:50 0|0:50:.:.:.:.:50
270
+ chrX 49075362 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||1|EntrezGene||||||||||1||||||||27|28|-2|2|0.02|0.00|0.01|0.99|WDR45|VUS|0.98327905|HP:0000951||XL|LP|||||||P|filter&vkgl&exit_p|,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|||EntrezGene||||||||||1||||||||27|28|-2|2|0.02|0.00|0.01|0.99|WDR45|VUS|0.98327905|HP:0000951||XL|LP|||||||P|filter&vkgl&exit_p|,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|0.0113522755|||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&exit_p|,T|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000906841|CTCF_binding_site||||||||||CS135341|1|||||||||||||||1|||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p| GT:DP:VI:VIC:VID:VIG:VIM:VIS:GQ:VIPC_S 0|0:10:.:.:.:.:.:.:50 0|0:50:.:.:.:.:.:.:50 0|0:50:.:.:.:.:.:.:50 1|0:50:XLD,XL,XLR:.:1:11152:1:XLD,XLR:50:U1 0|0:50:.:.:.:.:.:.:50 0|0:50:.:.:.:.:.:.:50
271
+ chrY 2787600 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|0.92795527|||||||||||P|filter&vkgl&clinVar&exit_p| GT:DP:VIC:VID:VIM:GQ:VIPC_S 0:10:.:.:.:50 .:.:.:.:.:50 1:50:.:.:.:50 1:50:.:1:0:50:U1 .:.:.:.:.:50 1:50:.:.:.:50
272
+ chrM 15325 mt_chrom A G . PASS CSQ=G|intergenic_variant|MODIFIER|||||||||||||||rs1556424568|1||||1||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p| GT:DP:VIC:VID:VIM:GQ:VIPC_S 0|0:10:.:.:.:50 0|0:50:.:.:.:50 0|0:50:.:.:.:50 1|0:50:.:1:0:50:U1 0|0:50:.:.:.:50 0|0:50:.:.:.:50
package/src/mocks/GRCh38/vcf/no_vep.vcf.blob CHANGED
@@ -3,6 +3,7 @@
3
3
  ##ALT=<ID=INS,Description="Insertion">
4
4
  ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
5
5
  ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
6
+ ##FORMAT=<ID=VIPC_S,Number=.,Type=String,Description="VIP decision tree classification.">
6
7
  ##INFO=<ID=BND_DEPTH,Number=1,Type=Integer,Description="Read depth at local translocation breakend">
7
8
  ##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakend">
8
9
  ##INFO=<ID=MATE_BND_DEPTH,Number=1,Type=Integer,Description="Read depth at remote translocation mate breakend">
@@ -208,31 +209,31 @@
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  ##fileDate=20200320
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  ##reference=file:/groups/umcg-gcc/tmp01/umcg-testdata/../vip/resources/GRCh38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz
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  #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Father Mother Nephew Patient Sister Unrelated
211
- chr1 9982480 . C T . PASS . GT:DP 0|0:10 0|0:50 0|0:50 1|0:50 0|0:50 0|0:50
212
- chr1 16049917 n_alt G N . PASS . GT:DP 1|0:11 0|0:50 0|0:50 0|1:10 0|0:50 0|0:50
213
- chr1 17022720 star_alt C * . PASS . GT:DP 0|0:50 0|0:50 0|0:50 1|0:50 0|0:50 0|0:50
214
- chr1 17022724 n_ref N A . PASS . GT:DP 1|0:50 0|0:50 0|0:50 1|0:50 0|0:50 0|0:50
215
- chr1 17022724 g_ref G A . PASS . GT:DP 1|0:50 0|0:50 0|0:50 1|0:50 0|0:50 0|0:50
216
- chr1 152548312 symbolic1 A <DEL> . PASS SVLEN=-49314;SVTYPE=DEL GT:DP 0|0:10 0|0:50 0|0:50 1|0:50 0|0:50 0|0:50
217
- chr2 47408528 symbolic2 G <INS> . PASS SVLEN=-49314;SVTYPE=INS GT:DP 0|0:10 0|0:50 0|0:50 1|0:50 0|0:50 0|0:50
218
- chr4 105399137 . G A . PASS . GT:DP 0|0:10 0|0:50 0|0:50 1|0:50 0|0:50 0|0:50
219
- chr7 41977712 single_breakend_nation C C. . PASS SVTYPE=BND GT:DP 0|0:10 0|0:50 0|0:50 1|0:50 0|0:50 0|0:50
220
- chr7 42025358 . GACTC G . PASS . GT:DP 0|0:10 0|0:50 0|0:50 1|0:50 0|0:50 0|0:50
221
- chr8 60852584 breakend1 G ]11:134014225]G . PASS BND_DEPTH=26;MATEID=breakend2;MATE_BND_DEPTH=39;SVTYPE=BND GT:DP 0|0:10 0|0:50 0|0:50 1|0:50 0|0:50 0|0:50
222
- chr8 144085597 . CAG C . PASS . GT:DP 0|0:10 0|0:50 0|0:50 1|0:50 0|0:50 0|0:50
223
- chr9 104784352 . AAAGAT A . PASS . GT:DP 0|0:10 0|0:50 0|0:50 1|0:50 0|0:50 0|0:50
224
- chr10 124402930 . G C . PASS . GT:DP 0|0:10 0|0:50 0|0:50 1|0:50 0|0:50 0|0:50
225
- chr11 134144330 breakend2 G G[8:61765143[ . PASS BND_DEPTH=39;MATEID=breakend1;MATE_BND_DEPTH=26;SVTYPE=BND GT:DP 0|0:10 0|0:50 0|0:50 1|0:50 0|0:50 0|0:50
226
- chr13 76995993 . G A . PASS . GT:DP 0|0:10 0|0:50 0|0:50 1|0:50 0|0:50 0|0:50
227
- chr14 88870063 . TG T . PASS . GT:DP 0|0:10 0|0:50 0|0:50 1|0:50 0|0:50 0|0:50
228
- chr14 104701523 . T G . PASS . GT:DP 0|0:10 0|0:50 0|0:50 1|0:50 0|0:50 0|0:50
229
- chr17 31229046 . AC A . PASS . GT:DP 0|0:10 0|0:50 0|0:50 1|0:50 0|0:50 0|0:50
230
- chr17 31336861 . T G . PASS . GT:DP 0|0:10 0|0:50 0|0:50 1|0:50 0|0:50 0|0:50
231
- chr19 11105470 . C G . PASS . GT:DP 0|0:10 0|0:50 0|0:50 1|0:50 0|0:50 0|0:50
232
- chr19 17341188 . GA G . PASS . GT:DP 0|0:10 0|0:50 0|0:50 1|0:50 0|0:50 0|0:50
233
- chr20 63695639 . C T . PASS . GT:DP 0|0:10 0|0:50 0|0:50 1|0:50 0|0:50 0|0:50
234
- chr22 50189164 . C CTG . PASS . GT:DP 0|0:10 0|0:50 0|0:50 1|0:50 0|0:50 0|0:50
235
- chr22 50283117 . C T . PASS . GT:DP 0|0:10 0|0:50 0|0:50 1|0:50 0|0:50 0|0:50
236
- chrX 49075362 x_chrom A T . PASS . GT:DP 0|0:10 0|0:50 0|0:50 1|0:50 0|0:50 0|0:50
237
- chrY 2787600 y_chrom G A . PASS . GT:DP 0:10 . 1:50 1:50 . 1:50
238
- chrM 15325 mt_chrom A G . PASS . GT:DP 0|0:10 0|0:50 0|0:50 1|0:50 0|0:50 0|0:50
212
+ chr1 9982480 . C T . PASS . GT:DP:VIPC_S 0|0:10 0|0:50 0|0:50 1|0:50:U1 0|0:50 0|0:50
213
+ chr1 16049917 n_alt G N . PASS . GT:DP:VIPC_S 1|0:11 0|0:50 0|0:50:U1 0|1:10 0|0:50 0|0:50
214
+ chr1 17022720 star_alt C * . PASS . GT:DP:VIPC_S 0|0:50 0|0:50 0|0:50 1|0:50:U1 0|0:50 0|0:50
215
+ chr1 17022724 n_ref N A . PASS . GT:DP:VIPC_S 1|0:50 0|0:50 0|0:50 1|0:50:U1 0|0:50 0|0:50
216
+ chr1 17022724 g_ref G A . PASS . GT:DP:VIPC_S 1|0:50 0|0:50 0|0:50 1|0:50:U1 0|0:50 0|0:50
217
+ chr1 152548312 symbolic1 A <DEL> . PASS SVLEN=-49314;SVTYPE=DEL GT:DP:VIPC_S 0|0:10 0|0:50 0|0:50 1|0:50:U1 0|0:50 0|0:50
218
+ chr2 47408528 symbolic2 G <INS> . PASS SVLEN=-49314;SVTYPE=INS GT:DP:VIPC_S 0|0:10 0|0:50 0|0:50 1|0:50:U1 0|0:50 0|0:50
219
+ chr4 105399137 . G A . PASS . GT:DP:VIPC_S 0|0:10 0|0:50 0|0:50 1|0:50:U1 0|0:50 0|0:50
220
+ chr7 41977712 single_breakend_nation C C. . PASS SVTYPE=BND GT:DP:VIPC_S 0|0:10 0|0:50 0|0:50 1|0:50:U1 0|0:50 0|0:50
221
+ chr7 42025358 . GACTC G . PASS . GT:DP:VIPC_S 0|0:10 0|0:50 0|0:50 1|0:50:U1 0|0:50 0|0:50
222
+ chr8 60852584 breakend1 G ]11:134014225]G . PASS BND_DEPTH=26;MATEID=breakend2;MATE_BND_DEPTH=39;SVTYPE=BND GT:DP:VIPC_S 0|0:10 0|0:50 0|0:50 1|0:50:U1 0|0:50 0|0:50
223
+ chr8 144085597 . CAG C . PASS . GT:DP:VIPC_S 0|0:10 0|0:50 0|0:50 1|0:50:U1 0|0:50 0|0:50
224
+ chr9 104784352 . AAAGAT A . PASS . GT:DP:VIPC_S 0|0:10 0|0:50 0|0:50 1|0:50:U1 0|0:50 0|0:50
225
+ chr10 124402930 . G C . PASS . GT:DP:VIPC_S 0|0:10 0|0:50 0|0:50 1|0:50:U1 0|0:50 0|0:50
226
+ chr11 134144330 breakend2 G G[8:61765143[ . PASS BND_DEPTH=39;MATEID=breakend1;MATE_BND_DEPTH=26;SVTYPE=BND GT:DP:VIPC_S 0|0:10 0|0:50 0|0:50 1|0:50:U1 0|0:50 0|0:50
227
+ chr13 76995993 . G A . PASS . GT:DP:VIPC_S 0|0:10 0|0:50 0|0:50 1|0:50:U1 0|0:50 0|0:50
228
+ chr14 88870063 . TG T . PASS . GT:DP:VIPC_S 0|0:10 0|0:50 0|0:50 1|0:50:U1 0|0:50 0|0:50
229
+ chr14 104701523 . T G . PASS . GT:DP:VIPC_S 0|0:10 0|0:50 0|0:50 1|0:50:U1 0|0:50 0|0:50
230
+ chr17 31229046 . AC A . PASS . GT:DP:VIPC_S 0|0:10 0|0:50 0|0:50 1|0:50:U1 0|0:50 0|0:50
231
+ chr17 31336861 . T G . PASS . GT:DP:VIPC_S 0|0:10 0|0:50 0|0:50 1|0:50:U1 0|0:50 0|0:50
232
+ chr19 11105470 . C G . PASS . GT:DP:VIPC_S 0|0:10 0|0:50 0|0:50 1|0:50:U1 0|0:50 0|0:50
233
+ chr19 17341188 . GA G . PASS . GT:DP:VIPC_S 0|0:10 0|0:50 0|0:50 1|0:50:U1 0|0:50 0|0:50
234
+ chr20 63695639 . C T . PASS . GT:DP:VIPC_S 0|0:10 0|0:50 0|0:50 1|0:50:U1 0|0:50 0|0:50
235
+ chr22 50189164 . C CTG . PASS . GT:DP:VIPC_S 0|0:10 0|0:50 0|0:50 1|0:50:U1 0|0:50 0|0:50
236
+ chr22 50283117 . C T . PASS . GT:DP:VIPC_S 0|0:10 0|0:50 0|0:50 1|0:50:U1 0|0:50 0|0:50
237
+ chrX 49075362 x_chrom A T . PASS . GT:DP:VIPC_S 0|0:10 0|0:50 0|0:50 1|0:50:U1 0|0:50 0|0:50
238
+ chrY 2787600 y_chrom G A . PASS . GT:DP:VIPC_S 0:10 . 1:50 1:50:U1 . 1:50
239
+ chrM 15325 mt_chrom A G . PASS . GT:DP:VIPC_S 0|0:10 0|0:50 0|0:50 1|0:50:U1 0|0:50 0|0:50