@molgenis/vip-report-template 7.1.2 → 8.0.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (156) hide show
  1. package/.gitattributes +3 -1
  2. package/.travis.yml +1 -0
  3. package/README.md +13 -0
  4. package/eslint.config.mjs +6 -1
  5. package/package.json +6 -5
  6. package/scripts/validateConfig/README.txt +5 -0
  7. package/scripts/validateConfig/compileValidator.ts +17 -0
  8. package/scripts/validateConfig/createSchema.ts +6 -0
  9. package/scripts/validateConfig/schema.ts +370 -0
  10. package/src/App.tsx +2 -1
  11. package/src/components/DatasetDropdown.tsx +1 -1
  12. package/src/components/GenomeBrowser.tsx +14 -4
  13. package/src/components/RecordsTable.tsx +23 -6
  14. package/src/components/VariantConsequenceContainer.tsx +9 -2
  15. package/src/components/VariantInfoTable.tsx +1 -1
  16. package/src/components/VariantsContainer.tsx +47 -9
  17. package/src/components/VariantsContainerHeader.tsx +1 -8
  18. package/src/components/field/composed/FieldGenotype.tsx +1 -1
  19. package/src/components/field/composed/FieldGenotypeStr.tsx +18 -10
  20. package/src/components/field/composed/FieldGnomAd.tsx +1 -1
  21. package/src/components/field/composed/FieldInheritanceModes.tsx +1 -4
  22. package/src/components/field/composed/FieldVkgl.tsx +1 -1
  23. package/src/components/field/typed/FieldCategorical.tsx +1 -1
  24. package/src/components/field/typed/FieldCharacter.tsx +1 -1
  25. package/src/components/field/typed/FieldFlag.tsx +1 -1
  26. package/src/components/field/typed/FieldFloat.tsx +1 -1
  27. package/src/components/field/typed/FieldInteger.tsx +1 -1
  28. package/src/components/field/typed/FieldString.tsx +1 -1
  29. package/src/components/filter/Filter.tsx +1 -0
  30. package/src/components/filter/composed/FilterAllelicImbalance.tsx +1 -0
  31. package/src/components/filter/composed/FilterComposed.tsx +7 -0
  32. package/src/components/filter/composed/FilterDeNovo.tsx +1 -0
  33. package/src/components/filter/composed/FilterHpo.tsx +1 -0
  34. package/src/components/filter/composed/FilterInheritance.tsx +1 -0
  35. package/src/components/filter/composed/FilterLocus.tsx +17 -3
  36. package/src/components/filter/composed/FilterPick.tsx +30 -0
  37. package/src/components/filter/composed/FilterVipC.tsx +1 -0
  38. package/src/components/filter/composed/FilterVipCS.tsx +1 -0
  39. package/src/components/filter/fixed/FilterFixed.tsx +7 -0
  40. package/src/components/filter/typed/FilterCategorical.tsx +18 -1
  41. package/src/components/filter/typed/FilterFlag.tsx +2 -0
  42. package/src/components/filter/typed/FilterInterval.tsx +29 -1
  43. package/src/components/filter/typed/FilterString.tsx +8 -1
  44. package/src/components/filter/typed/FilterTyped.tsx +1 -0
  45. package/src/components/form/ButtonApply.tsx +6 -2
  46. package/src/mocks/GRCh38/README.txt +15 -0
  47. package/src/mocks/GRCh38/decisionTree.json +201 -0
  48. package/src/mocks/GRCh38/family.ped +6 -0
  49. package/src/mocks/GRCh38/field_metadata.json +36 -11
  50. package/src/mocks/GRCh38/sample1.ped +1 -0
  51. package/src/mocks/GRCh38/static.ts +36 -148
  52. package/src/mocks/GRCh38/str.ped +1 -0
  53. package/src/mocks/GRCh38/vcf/family.db.blob +0 -0
  54. package/src/mocks/GRCh38/vcf/family.vcf +312 -0
  55. package/src/mocks/GRCh38/vcf/fixPaths.sql +7 -0
  56. package/src/mocks/GRCh38/vcf/no_vep.db.blob +0 -0
  57. package/src/mocks/GRCh38/vcf/{no_vep.vcf.blob → no_vep.vcf} +1 -1
  58. package/src/mocks/GRCh38/vcf/samples_0.db.blob +0 -0
  59. package/src/mocks/GRCh38/vcf/samples_1.db.blob +0 -0
  60. package/src/mocks/GRCh38/vcf/samples_100.db.blob +0 -0
  61. package/src/mocks/GRCh38/vcf/{samples_100.vcf.blob → samples_100.vcf} +6 -6
  62. package/src/mocks/GRCh38/vcf/str.db.blob +0 -0
  63. package/src/mocks/GRCh38/vcf/{str.vcf.blob → str.vcf} +17 -17
  64. package/src/mocks/MockApiClient.ts +60 -226
  65. package/src/mocks/config_cram.json +4 -0
  66. package/src/mocks/config_default_values.json +722 -0
  67. package/src/mocks/config_vcf.json +15 -1
  68. package/src/mocks/sql-wasm.wasm.blob +0 -0
  69. package/src/types/config.d.ts +9 -5
  70. package/src/types/configCells.d.ts +1 -0
  71. package/src/types/configFilter.d.ts +1 -0
  72. package/src/types/configFilterComposed.d.ts +3 -0
  73. package/src/utils/api.ts +21 -49
  74. package/src/utils/config/configCellsComposed.ts +1 -1
  75. package/src/utils/config/configCellsField.ts +2 -0
  76. package/src/utils/config/configFiltersComposed.ts +7 -0
  77. package/src/utils/config/configFiltersField.ts +3 -2
  78. package/src/utils/config/configFiltersFixed.ts +7 -0
  79. package/src/utils/config/configValidator.precompiled.ts +83402 -0
  80. package/src/utils/config/configValidator.ts +3 -368
  81. package/src/utils/csq.ts +5 -10
  82. package/src/utils/decisionTree.ts +8 -9
  83. package/src/utils/query/query.ts +3 -2
  84. package/src/utils/query/queryFilter.ts +2 -3
  85. package/src/utils/query/queryFilterComposed.ts +12 -12
  86. package/src/utils/query/queryFilterField.ts +14 -7
  87. package/src/utils/query/queryFilterFixed.ts +5 -5
  88. package/src/utils/query/querySample.ts +15 -4
  89. package/src/utils/query/selector.ts +5 -20
  90. package/src/utils/query/sort.ts +4 -4
  91. package/src/utils/vcf.ts +20 -11
  92. package/src/views/Help.tsx +2 -2
  93. package/src/views/SampleVariant.tsx +4 -1
  94. package/src/views/Samples.tsx +10 -3
  95. package/src/views/data/data.tsx +2 -2
  96. package/tests/utils/config/configFiltersComposed.test.ts +2 -0
  97. package/tests/utils/config/configFiltersField.test.ts +4 -2
  98. package/tests/utils/config/configFiltersFixed.test.ts +23 -6
  99. package/tests/utils/query/query.test.ts +34 -6
  100. package/tests/utils/query/queryFilter.test.ts +4 -31
  101. package/tests/utils/query/queryFilterComposed.test.ts +13 -13
  102. package/tests/utils/query/queryFilterField.test.ts +5 -5
  103. package/tests/utils/query/queryFilterFixed.test.ts +5 -5
  104. package/tests/utils/query/querySample.test.ts +50 -10
  105. package/tests/utils/query/sort.test.ts +1 -1
  106. package/tests/utils/vcf.test.ts +1 -0
  107. package/vite.config.mts +2 -1
  108. package/src/mocks/GRCh37/alignment.cram.blob +0 -0
  109. package/src/mocks/GRCh37/alignment.cram.crai.blob +0 -0
  110. package/src/mocks/GRCh37/decisionTree.json +0 -355
  111. package/src/mocks/GRCh37/fasta/1-10042288-10042788.fasta.gz.blob +0 -0
  112. package/src/mocks/GRCh37/fasta/1-152520538-152521038.fasta.gz.blob +0 -0
  113. package/src/mocks/GRCh37/fasta/1-16375333-16375833.fasta.gz.blob +0 -0
  114. package/src/mocks/GRCh37/fasta/1-16376162-16376662.fasta.gz.blob +0 -0
  115. package/src/mocks/GRCh37/fasta/1-17348965-17349469.fasta.gz.blob +0 -0
  116. package/src/mocks/GRCh37/fasta/1-17348969-17349469.fasta.gz.blob +0 -0
  117. package/src/mocks/GRCh37/fasta/1-17354844-17355344.fasta.gz.blob +0 -0
  118. package/src/mocks/GRCh37/fasta/10-126091249-126091749.fasta.gz.blob +0 -0
  119. package/src/mocks/GRCh37/fasta/11-134013975-134014475.fasta.gz.blob +0 -0
  120. package/src/mocks/GRCh37/fasta/13-77569878-77570378.fasta.gz.blob +0 -0
  121. package/src/mocks/GRCh37/fasta/14-105167610-105168110.fasta.gz.blob +0 -0
  122. package/src/mocks/GRCh37/fasta/14-89307588-89308088.fasta.gz.blob +0 -0
  123. package/src/mocks/GRCh37/fasta/14-89309945-89310445.fasta.gz.blob +0 -0
  124. package/src/mocks/GRCh37/fasta/14-89336157-89336657.fasta.gz.blob +0 -0
  125. package/src/mocks/GRCh37/fasta/17-29555814-29556314.fasta.gz.blob +0 -0
  126. package/src/mocks/GRCh37/fasta/17-29585172-29585672.fasta.gz.blob +0 -0
  127. package/src/mocks/GRCh37/fasta/17-29663629-29664129.fasta.gz.blob +0 -0
  128. package/src/mocks/GRCh37/fasta/17-29675976-29676476.fasta.gz.blob +0 -0
  129. package/src/mocks/GRCh37/fasta/17-29683733-29684233.fasta.gz.blob +0 -0
  130. package/src/mocks/GRCh37/fasta/19-11215896-11216396.fasta.gz.blob +0 -0
  131. package/src/mocks/GRCh37/fasta/19-11223801-11224301.fasta.gz.blob +0 -0
  132. package/src/mocks/GRCh37/fasta/19-17449149-17449649.fasta.gz.blob +0 -0
  133. package/src/mocks/GRCh37/fasta/19-17451747-17452247.fasta.gz.blob +0 -0
  134. package/src/mocks/GRCh37/fasta/2-47635417-47635917.fasta.gz.blob +0 -0
  135. package/src/mocks/GRCh37/fasta/20-62326742-62327242.fasta.gz.blob +0 -0
  136. package/src/mocks/GRCh37/fasta/22-50627343-50627843.fasta.gz.blob +0 -0
  137. package/src/mocks/GRCh37/fasta/22-50721296-50721796.fasta.gz.blob +0 -0
  138. package/src/mocks/GRCh37/fasta/4-106320044-106320544.fasta.gz.blob +0 -0
  139. package/src/mocks/GRCh37/fasta/7-42017061-42017561.fasta.gz.blob +0 -0
  140. package/src/mocks/GRCh37/fasta/7-42064707-42065207.fasta.gz.blob +0 -0
  141. package/src/mocks/GRCh37/fasta/8-145140250-145140750.fasta.gz.blob +0 -0
  142. package/src/mocks/GRCh37/fasta/8-61764893-61765393.fasta.gz.blob +0 -0
  143. package/src/mocks/GRCh37/fasta/9-107546383-107546883.fasta.gz.blob +0 -0
  144. package/src/mocks/GRCh37/fasta/9-107584614-107585114.fasta.gz.blob +0 -0
  145. package/src/mocks/GRCh37/fasta/MT-15076-15576.fasta.gz.blob +0 -0
  146. package/src/mocks/GRCh37/fasta/X-48932771-48933271.fasta.gz.blob +0 -0
  147. package/src/mocks/GRCh37/fasta/Y-2655391-2655891.fasta.gz.blob +0 -0
  148. package/src/mocks/GRCh37/field_metadata.json +0 -794
  149. package/src/mocks/GRCh37/genes.gff.gz.blob +0 -0
  150. package/src/mocks/GRCh37/sampleTree.json +0 -143
  151. package/src/mocks/GRCh37/static.ts +0 -189
  152. package/src/mocks/GRCh37/vcf/family.vcf.blob +0 -134
  153. package/src/mocks/GRCh38/vcf/family.vcf.blob +0 -272
  154. package/src/mocks/static.ts +0 -1636
  155. /package/src/mocks/GRCh38/vcf/{samples_0.vcf.blob → samples_0.vcf} +0 -0
  156. /package/src/mocks/GRCh38/vcf/{samples_1.vcf.blob → samples_1.vcf} +0 -0
package/src/mocks/GRCh38/vcf/{samples_100.vcf.blob → samples_100.vcf} RENAMED
@@ -241,10 +241,10 @@
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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:VIPC_S 1|1:U1 0|1:U1 0/0:U1 0|0:U1 0/1:U1 0|0:U1 1|1:U1 0/0:U1 1/0:U1 0/1:U1 1|1:U1 1/0:U1 1/1:U1 0/0:U1 1|0:U1 0/1:U1 0|1:U1 0/0:U1 0/0:U1 1/0:U1 1|0:U1 1|0:U1 1/0:U1 0|1:U1 1|1:U1 1/0:U1 0/0:U1 1|0:U1 0/0:U1 0/0:U1 1|1:U1 0/0:U1 1|1:U1 1/0:U1 0|0:U1 0/0:U1 1|0:U1 0/0:U1 1/1:U1 1|1:U1 0/1:U1 0/0:U1 1|1:U1 1|1:U1 1|0:U1 0|1:U1 1|0:U1 0|0:U1 1/0:U1 0|0:U1 0/0:U1 1|0:U1 1/1:U1 1/1:U1 0/0:U1 0/0:U1 0|1:U1 0/0:U1 1/0:U1 0|0:U1 0/1:U1 1|0:U1 1|1:U1 1|0:U1 0/0:U1 0|0:U1 1/0:U1 1|0:U1 0/0:U1 1|0:U1 1|1:U1 0/1:U1 0/0:U1 1|1:U1 1/0:U1 1/1:U1 0/0:U1 0|0:U1 1|0:U1 0|0:U1 0/0:U1 0|0:U1 0/0:U1 0|0:U1 0/0:U1 0/0:U1 0/1:U1 1/0:U1 0/0:U1 0/1:U1 0|1:U1 1/0:U1 1|0:U1 0|0:U1 0/0:U1 0/1:U1 1/0:U1 0|1:U1 1/1:U1 1/0:U1
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  chr1 16049917 n_alt G N . PASS CSQ=N|splice_donor_variant|HIGH|CLCNKB|1188|Transcript|NM_000085.5|protein_coding||10/19||||||||CS1211892&CS971662|1||1||1|EntrezGene||||||||||1&1|||||||||||||||||VUS|0.45317215|HP:0000951||AR||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,N|splice_donor_variant|HIGH|CLCNKB|1188|Transcript|NM_001165945.2|protein_coding||3/12||||||||CS1211892&CS971662|1||1|||EntrezGene||||||||||1&1|||||||||||||||||VUS|0.45317215|HP:0000951||AR||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p| GT:VIPC_S 1/0:U1 0/1:U1 0|1:U1 0/0:U1 0|0:U1 1/0:U1 0|0:U1 1|1:U1 1|0:U1 1|1:U1 0/0:U1 0|0:U1 0/0:U1 1/0:U1 0/0:U1 1|0:U1 1|0:U1 0|1:U1 0/1:U1 1/0:U1 0/0:U1 0|1:U1 1|0:U1 1|1:U1 0|0:U1 0/1:U1 0/1:U1 0|0:U1 0/0:U1 0|1:U1 1/1:U1 1/0:U1 1/1:U1 0/0:U1 1/0:U1 0|1:U1 0/1:U1 0|0:U1 0/1:U1 0|0:U1 1/0:U1 1/1:U1 0/1:U1 1|0:U1 0/1:U1 0|0:U1 1|0:U1 0/0:U1 0/0:U1 1/0:U1 1/0:U1 1|0:U1 1/0:U1 0|0:U1 0/0:U1 1/1:U1 0|0:U1 0|0:U1 0/0:U1 0/1:U1 1/0:U1 0|0:U1 1/0:U1 0/0:U1 0|1:U1 0|1:U1 0/1:U1 0/0:U1 0/0:U1 0/1:U1 1/0:U1 1/0:U1 1|1:U1 0/0:U1 1/0:U1 0/1:U1 0|1:U1 1/0:U1 0|1:U1 0|0:U1 1/0:U1 1|1:U1 0/1:U1 0/1:U1 1|0:U1 1/0:U1 1|1:U1 1|0:U1 0|0:U1 1|1:U1 0/1:U1 1|0:U1 0|1:U1 0/0:U1 0|0:U1 0|0:U1 0/0:U1 1|0:U1 1|0:U1 1/1:U1
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  chr1 17022724 n_ref N A . PASS CSQ=A|coding_sequence_variant|MODIFIER|SDHB|6390|Transcript|NM_003000.3|protein_coding|7/8||NM_003000.3:c.649C>T||662/1015|649/843|217/280||Ngc/Tgc|CM1210440&CM094752|1||-1||1|EntrezGene||||||||||1&1|||||||||||||||||VUS|0.20536129|HP:0000951||AD&AR||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p| GT:VIPC_S 0/0:U1 0/0:U1 0/0:U1 1|1:U1 0/1:U1 0|1:U1 1|0:U1 1|1:U1 0|0:U1 0/0:U1 1|1:U1 1|0:U1 0|0:U1 0|0:U1 1|0:U1 0|1:U1 0/0:U1 1|1:U1 0/1:U1 1/0:U1 1|1:U1 0|0:U1 1/0:U1 0/1:U1 0|0:U1 0|0:U1 0|1:U1 0/1:U1 0|0:U1 0/0:U1 0|0:U1 0|1:U1 0/0:U1 0/0:U1 0/1:U1 1|1:U1 0/0:U1 0|0:U1 1/1:U1 1/0:U1 0/1:U1 0/1:U1 0|0:U1 1|0:U1 0/0:U1 1|0:U1 0/0:U1 0|0:U1 0|1:U1 0|0:U1 1|0:U1 0|1:U1 0/1:U1 0|0:U1 1|0:U1 0|1:U1 0|0:U1 0|0:U1 1/0:U1 0/0:U1 1/0:U1 1|1:U1 0/0:U1 1/0:U1 1|0:U1 0|0:U1 1/0:U1 1/1:U1 1/1:U1 1/1:U1 0/1:U1 0|0:U1 0/1:U1 0|0:U1 1/0:U1 0|0:U1 1/0:U1 0/0:U1 0/1:U1 0|0:U1 0|1:U1 1/0:U1 0/0:U1 0|1:U1 0|0:U1 0/1:U1 0|0:U1 0|0:U1 0|1:U1 1/0:U1 0/0:U1 0|1:U1 1|1:U1 1/1:U1 0/1:U1 0|0:U1 1/0:U1 0|0:U1 1/0:U1 1/0:U1
244
- chr1 17022724 g_ref G A . PASS CSQ=A|missense_variant|MODERATE|SDHB|6390|Transcript|NM_003000.3|protein_coding|7/8||NM_003000.3:c.649C>T|NP_002991.2:p.Arg217Cys|662/1015|649/843|217/280|R/C|Cgc/Tgc|rs200245469&CM1210440&CM094752|1||-1||1|EntrezGene|||||0|1:U1||pathogenic&likely_pathogenic||1&1&1||||||||28|6|6|5|0.00|0.00|0.00|0.00|SDHB|VUS|0.88626856|HP:0000951||AD&AR|LP||||chr1:17022724-17022724|6.57186e-06|0|P|filter&vkgl&exit_p| GT:VIPC_S 1/0:U1 0/1:U1 0/1:U1 1|1:U1 1|0:U1 0|1:U1 1|0:U1 0/0:U1 1|1:U1 1|0:U1 0|0:U1 0|0:U1 0|1:U1 0|1:U1 0/0:U1 1/1:U1 0|0:U1 0/1:U1 0/1:U1 1|1:U1 0|1:U1 1|1:U1 0/0:U1 0/0:U1 0|1:U1 1/1:U1 0|1:U1 0/1:U1 0/0:U1 0|1:U1 0/0:U1 1/0:U1 0/0:U1 0|1:U1 0|1:U1 0/0:U1 0/0:U1 0/0:U1 0|0:U1 0/0:U1 0|1:U1 1|0:U1 0/0:U1 0|1:U1 0|1:U1 0|0:U1 0/0:U1 0|1:U1 0|0:U1 1/1:U1 1|1:U1 0|0:U1 1|1:U1 0/0:U1 0|0:U1 0|1:U1 1/0:U1 0/1:U1 0/0:U1 0|0:U1 1|0:U1 0|0:U1 0|0:U1 0|1:U1 0|1:U1 0/0:U1 1/0:U1 1|1:U1 0|0:U1 0/0:U1 1/1:U1 0/0:U1 0/0:U1 0/0:U1 0/0:U1 0|0:U1 0|1:U1 0|1:U1 0/0:U1 0/0:U1 1|0:U1 0/1:U1 0/1:U1 1/0:U1 0|0:U1 0/1:U1 0/1:U1 0/0:U1 1/1:U1 1|0:U1 1/0:U1 1/1:U1 0|0:U1 0/0:U1 1|0:U1 1/0:U1 0|0:U1 1/0:U1 1|1:U1 0|1:U1
244
+ chr1 17022724 g_ref G A . PASS CSQ=A|missense_variant|MODERATE|SDHB|6390|Transcript|NM_003000.3|protein_coding|7/8||NM_003000.3:c.649C>T|NP_002991.2:p.Arg217Cys|662/1015|649/843|217/280|R/C|Cgc/Tgc|rs200245469&CM1210440&CM094752|1||-1||1|EntrezGene|||||0|0.001||pathogenic&likely_pathogenic||1&1&1||||||||28|6|6|5|0.00|0.00|0.00|0.00|SDHB|VUS|0.88626856|HP:0000951||AD&AR|LP||||chr1:17022724-17022724|6.57186e-06|0|P|filter&vkgl&exit_p| GT:VIPC_S 1/0:U1 0/1:U1 0/1:U1 1|1:U1 1|0:U1 0|1:U1 1|0:U1 0/0:U1 1|1:U1 1|0:U1 0|0:U1 0|0:U1 0|1:U1 0|1:U1 0/0:U1 1/1:U1 0|0:U1 0/1:U1 0/1:U1 1|1:U1 0|1:U1 1|1:U1 0/0:U1 0/0:U1 0|1:U1 1/1:U1 0|1:U1 0/1:U1 0/0:U1 0|1:U1 0/0:U1 1/0:U1 0/0:U1 0|1:U1 0|1:U1 0/0:U1 0/0:U1 0/0:U1 0|0:U1 0/0:U1 0|1:U1 1|0:U1 0/0:U1 0|1:U1 0|1:U1 0|0:U1 0/0:U1 0|1:U1 0|0:U1 1/1:U1 1|1:U1 0|0:U1 1|1:U1 0/0:U1 0|0:U1 0|1:U1 1/0:U1 0/1:U1 0/0:U1 0|0:U1 1|0:U1 0|0:U1 0|0:U1 0|1:U1 0|1:U1 0/0:U1 1/0:U1 1|1:U1 0|0:U1 0/0:U1 1/1:U1 0/0:U1 0/0:U1 0/0:U1 0/0:U1 0|0:U1 0|1:U1 0|1:U1 0/0:U1 0/0:U1 1|0:U1 0/1:U1 0/1:U1 1/0:U1 0|0:U1 0/1:U1 0/1:U1 0/0:U1 1/1:U1 1|0:U1 1/0:U1 1/1:U1 0|0:U1 0/0:U1 1|0:U1 1/0:U1 0|0:U1 1/0:U1 1|1:U1 0|1:U1
245
245
  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:VIPC_S 0/0:U1 1/0:U1 1/0:U1 0|0:U1 1/1:U1 0|0:U1 0/0:U1 1/1:U1 1/1:U1 0|1:U1 1|1:U1 0|1:U1 0/0:U1 1|1:U1 1/0:U1 1/1:U1 0|0:U1 1|0:U1 0|1:U1 1|0:U1 1|1:U1 0/1:U1 0/0:U1 0/0:U1 0/0:U1 0|1:U1 1/1:U1 0/0:U1 0|0:U1 0/0:U1 0|0:U1 0/0:U1 0/1:U1 1/0:U1 0/0:U1 0|0:U1 1/1:U1 0|1:U1 1|0:U1 1|1:U1 0|1:U1 1|0:U1 1/1:U1 1/0:U1 0|0:U1 1|1:U1 0|0:U1 0/1:U1 0|0:U1 0/0:U1 0/0:U1 1/1:U1 0|0:U1 0|1:U1 1/0:U1 1/0:U1 0|0:U1 1|0:U1 0|0:U1 0/1:U1 1|0:U1 1|1:U1 1|0:U1 1|0:U1 0|1:U1 1|0:U1 0/0:U1 0|0:U1 0/0:U1 1/0:U1 0|0:U1 0/0:U1 0/0:U1 1/0:U1 0|0:U1 0/1:U1 0/1:U1 1/0:U1 1/1:U1 1|1:U1 0|0:U1 0/0:U1 0|0:U1 0|1:U1 0/0:U1 0/0:U1 0/0:U1 1/0:U1 0/1:U1 1|0:U1 0/0:U1 0/0:U1 1|0:U1 0|0:U1 0/0:U1 0/1:U1 1/0:U1 0|0:U1 0|0:U1 0/0:U1
246
246
  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:VIPC_S 1|1:U1 1/0:U1 1|1:U1 0/1:U1 1/1:U1 1/0:U1 1/1:U1 1|1:U1 0|0:U1 0|1:U1 0|0:U1 0|0:U1 1|0:U1 0/0:U1 1|1:U1 0/0:U1 1|0:U1 1|0:U1 0/1:U1 1|0:U1 0|1:U1 0/0:U1 1|1:U1 0|0:U1 1|1:U1 1|0:U1 0/0:U1 1|0:U1 0/1:U1 0/0:U1 0|1:U1 0/1:U1 0/1:U1 1/0:U1 1/0:U1 0|0:U1 1/0:U1 0|1:U1 0/0:U1 0|1:U1 0/1:U1 0|1:U1 0|1:U1 0|0:U1 0/1:U1 0|0:U1 1|0:U1 1|1:U1 0/1:U1 0|0:U1 0|0:U1 0|0:U1 0/0:U1 0/0:U1 0/1:U1 1|1:U1 0|0:U1 0|0:U1 0|0:U1 0|0:U1 0|0:U1 1/0:U1 1|0:U1 1/0:U1 0|1:U1 0/1:U1 0/0:U1 1|0:U1 0/0:U1 0/0:U1 0/1:U1 1/1:U1 0|0:U1 0|0:U1 0|0:U1 1/0:U1 0/1:U1 1|1:U1 0/1:U1 1/1:U1 0/0:U1 0/0:U1 1/1:U1 0|0:U1 1|0:U1 0|0:U1 0|1:U1 0/0:U1 1/0:U1 1/1:U1 1|0:U1 1/1:U1 0/1:U1 0|1:U1 0|0:U1 0|0:U1 0/1:U1 1|1:U1 0|1:U1 1/1:U1
247
- 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:U1.985||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:U1.992||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:U1.995||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:U1.993||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:VIPC_S 0/0:U1 1|1:U1 0/1:U1 0|0:U1 0|0:U1 1|0:U1 1/0:U1 1|0:U1 1|0:U1 1|0:U1 0/1:U1 0|0:U1 0/0:U1 0|0:U1 0/0:U1 1|0:U1 0/1:U1 1|0:U1 0|0:U1 0/0:U1 0/0:U1 0|0:U1 0|0:U1 0|0:U1 1|1:U1 0|0:U1 1|0:U1 0/0:U1 0|1:U1 0|1:U1 0|1:U1 0/1:U1 1|0:U1 0|1:U1 0/0:U1 1/1:U1 0|1:U1 0/0:U1 1/1:U1 1/0:U1 1|0:U1 0/1:U1 1|0:U1 0/0:U1 1|0:U1 0/0:U1 0|1:U1 0|1:U1 1|0:U1 0/0:U1 0|0:U1 0|0:U1 1/0:U1 0|0:U1 1/1:U1 0|0:U1 1|1:U1 0/1:U1 0|0:U1 0|1:U1 0/0:U1 1/0:U1 1|0:U1 0/1:U1 0|0:U1 0|0:U1 0/1:U1 0|1:U1 0/1:U1 0|1:U1 0/0:U1 1/0:U1 0/1:U1 1/0:U1 0/1:U1 0|0:U1 1/0:U1 1|0:U1 0/1:U1 0/0:U1 1/1:U1 0/0:U1 0|0:U1 0/0:U1 0/0:U1 0/1:U1 0/1:U1 0|0:U1 1/1:U1 0/1:U1 0/0:U1 0/0:U1 1|0:U1 1/0:U1 0/0:U1 0/0:U1 0/0:U1 1/1:U1 0/1:U1 0|1:U1
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+ 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:VIPC_S 0/0:U1 1|1:U1 0/1:U1 0|0:U1 0|0:U1 1|0:U1 1/0:U1 1|0:U1 1|0:U1 1|0:U1 0/1:U1 0|0:U1 0/0:U1 0|0:U1 0/0:U1 1|0:U1 0/1:U1 1|0:U1 0|0:U1 0/0:U1 0/0:U1 0|0:U1 0|0:U1 0|0:U1 1|1:U1 0|0:U1 1|0:U1 0/0:U1 0|1:U1 0|1:U1 0|1:U1 0/1:U1 1|0:U1 0|1:U1 0/0:U1 1/1:U1 0|1:U1 0/0:U1 1/1:U1 1/0:U1 1|0:U1 0/1:U1 1|0:U1 0/0:U1 1|0:U1 0/0:U1 0|1:U1 0|1:U1 1|0:U1 0/0:U1 0|0:U1 0|0:U1 1/0:U1 0|0:U1 1/1:U1 0|0:U1 1|1:U1 0/1:U1 0|0:U1 0|1:U1 0/0:U1 1/0:U1 1|0:U1 0/1:U1 0|0:U1 0|0:U1 0/1:U1 0|1:U1 0/1:U1 0|1:U1 0/0:U1 1/0:U1 0/1:U1 1/0:U1 0/1:U1 0|0:U1 1/0:U1 1|0:U1 0/1:U1 0/0:U1 1/1:U1 0/0:U1 0|0:U1 0/0:U1 0/0:U1 0/1:U1 0/1:U1 0|0:U1 1/1:U1 0/1:U1 0/0:U1 0/0:U1 1|0:U1 1/0:U1 0/0:U1 0/0:U1 0/0:U1 1/1:U1 0/1:U1 0|1:U1
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  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:VIPC_S 1/0:U1 1|0:U1 0/0:U1 0|1:U1 0/1:U1 1|0:U1 0|0:U1 1|0:U1 0/0:U1 1|0:U1 0/0:U1 1/0:U1 0|1:U1 1|0:U1 0/0:U1 1|0:U1 1/0:U1 0|1:U1 1|1:U1 0|1:U1 0|1:U1 1|1:U1 1|0:U1 0|1:U1 1|0:U1 1|0:U1 0|0:U1 0/0:U1 0|1:U1 1/1:U1 0|1:U1 0/0:U1 0|0:U1 0/1:U1 1/0:U1 1/0:U1 0|0:U1 0|1:U1 0|1:U1 0/0:U1 0/1:U1 0/1:U1 0/0:U1 0|1:U1 0/1:U1 0/0:U1 0/0:U1 1|0:U1 0|1:U1 1|0:U1 0/0:U1 1|0:U1 1|0:U1 1/0:U1 1|1:U1 0|0:U1 0|0:U1 0|1:U1 1|0:U1 0/1:U1 1/1:U1 0/1:U1 0/1:U1 1/1:U1 1|0:U1 0/0:U1 1/0:U1 0/0:U1 1/0:U1 0/0:U1 0|0:U1 1/0:U1 1/0:U1 1/1:U1 0/0:U1 1|1:U1 1/0:U1 0|0:U1 0/0:U1 1/0:U1 0|0:U1 0/1:U1 1|1:U1 0/0:U1 1/1:U1 1|1:U1 1|0:U1 0|1:U1 0|0:U1 1/0:U1 0/1:U1 0|0:U1 1|1:U1 1/0:U1 1/0:U1 0/0:U1 0/1:U1 1|1:U1 0|0:U1 1/0:U1
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  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:VIPC_S 1|0:U1 0/1:U1 0|1:U1 0|0:U1 1/0:U1 0|0:U1 0|1:U1 0/0:U1 0/0:U1 1/0:U1 0|1:U1 0|0:U1 0/1:U1 1/0:U1 1|0:U1 0/1:U1 0/0:U1 1/1:U1 0/0:U1 0/1:U1 0/0:U1 0/1:U1 1|1:U1 0/0:U1 1/0:U1 0/0:U1 1|1:U1 0|1:U1 0|1:U1 0|0:U1 0|0:U1 1/0:U1 0|0:U1 0|0:U1 0|0:U1 0/1:U1 1/0:U1 0|0:U1 0/0:U1 0|0:U1 0|0:U1 0|0:U1 0/1:U1 0/1:U1 0|1:U1 1/0:U1 0|0:U1 0|0:U1 0/0:U1 0/0:U1 1/1:U1 0/0:U1 0|0:U1 0|0:U1 1|0:U1 0|1:U1 0|1:U1 0/1:U1 0/0:U1 0/0:U1 1|0:U1 1|1:U1 1/0:U1 0|0:U1 1/1:U1 1/0:U1 0/0:U1 0/1:U1 0|1:U1 1|0:U1 0|1:U1 1|0:U1 0|0:U1 0/0:U1 1|1:U1 0|0:U1 0/0:U1 1|1:U1 1|0:U1 0|0:U1 0/0:U1 1/0:U1 0|1:U1 0|0:U1 0|0:U1 1|0:U1 0/1:U1 0/0:U1 0/0:U1 0/1:U1 0|1:U1 0|0:U1 0|0:U1 0/1:U1 0/0:U1 0|1:U1 0|0:U1 0/1:U1 0|1:U1 0/0:U1
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  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:VIPC_S 0/1:U1 0|0:U1 0/1:U1 0/1:U1 0|0:U1 1|1:U1 0/1:U1 0/0:U1 1|0:U1 0|0:U1 0/0:U1 0|1:U1 1/1:U1 1|0:U1 1/1:U1 1|0:U1 0|0:U1 0|1:U1 0/1:U1 1|1:U1 0/1:U1 0/0:U1 0|1:U1 0|0:U1 0|0:U1 1|1:U1 0|0:U1 0/1:U1 0/1:U1 0|1:U1 0/0:U1 0|1:U1 0/0:U1 0/1:U1 0|1:U1 1/0:U1 1|0:U1 1|0:U1 0/0:U1 0/0:U1 0/0:U1 0|0:U1 0|1:U1 1|0:U1 1/0:U1 0/0:U1 0|0:U1 0|1:U1 0/0:U1 0|1:U1 0/0:U1 0|0:U1 1/1:U1 0/1:U1 0/0:U1 1|0:U1 0/1:U1 1|0:U1 0/0:U1 1/1:U1 0/0:U1 1|1:U1 1/0:U1 0|0:U1 1|0:U1 0|1:U1 1/0:U1 0/1:U1 1/0:U1 1|1:U1 0|1:U1 0|0:U1 1/1:U1 1|1:U1 1/0:U1 0/0:U1 0|1:U1 1/1:U1 0/1:U1 0|1:U1 1|1:U1 1/1:U1 1|1:U1 0/1:U1 0|0:U1 0/0:U1 0/1:U1 1/0:U1 0|0:U1 0|1:U1 0|0:U1 0/0:U1 1|0:U1 0/1:U1 0/0:U1 0|0:U1 0|1:U1 0|0:U1 0/1:U1 0|0:U1
@@ -252,16 +252,16 @@ chr8 144085597 . CAG C . PASS CSQ=-|frameshift_variant|HIGH|GPAA1|8733|Transcrip
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  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:VIPC_S 0|1:U1 0/1:U1 0/0:U1 1/0:U1 0|0:U1 0/0:U1 0/0:U1 0/1:U1 0/0:U1 1/1:U1 0|1:U1 1/0:U1 0/1:U1 0/1:U1 0|0:U1 0|0:U1 0/1:U1 0|0:U1 1/0:U1 0|0:U1 0|0:U1 1|0:U1 1|0:U1 0|0:U1 1/1:U1 0/1:U1 0|0:U1 0|1:U1 0/1:U1 0|1:U1 0/1:U1 0|0:U1 0|0:U1 0/0:U1 1|0:U1 0/1:U1 0/1:U1 0/0:U1 0|1:U1 1|1:U1 1/0:U1 1|1:U1 0|0:U1 1/0:U1 0|1:U1 1|0:U1 0|1:U1 0/0:U1 0/0:U1 1/0:U1 1/0:U1 0/1:U1 1/1:U1 1|1:U1 1|0:U1 0|0:U1 0|1:U1 0|0:U1 1/0:U1 0|0:U1 0|0:U1 0|0:U1 1/1:U1 1|0:U1 1/1:U1 1/1:U1 1/0:U1 0|1:U1 0|0:U1 1|0:U1 0/0:U1 0|0:U1 0/1:U1 0|0:U1 0/0:U1 0|1:U1 1/1:U1 1|0:U1 1|0:U1 0/0:U1 1/0:U1 1|1:U1 1|0:U1 1/0:U1 0|1:U1 0|0:U1 0|1:U1 1|1:U1 0|0:U1 0/0:U1 0/1:U1 0|0:U1 1|0:U1 0|1:U1 0/0:U1 1|0:U1 0/0:U1 1/0:U1 0|0:U1 0|0:U1
253
253
  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:VIPC_S 1/0:U1 0/1:U1 1|0:U1 0/0:U1 0/0:U1 1/1:U1 1/1:U1 0|0:U1 1/1:U1 0|0:U1 0|0:U1 0/0:U1 0|1:U1 0|0:U1 0/1:U1 0|1:U1 1/1:U1 0|0:U1 0/0:U1 0|0:U1 1|1:U1 0/0:U1 0|0:U1 0/0:U1 1/0:U1 1/0:U1 0/0:U1 1|1:U1 1/0:U1 1/0:U1 0/0:U1 0/0:U1 0|1:U1 0/1:U1 0|0:U1 1|1:U1 1/0:U1 1/1:U1 0/0:U1 1|0:U1 1/0:U1 1|0:U1 0|1:U1 1|0:U1 0|0:U1 1/0:U1 1/0:U1 0|0:U1 1/1:U1 0|1:U1 1|1:U1 0/0:U1 0|0:U1 1/0:U1 0/0:U1 1/0:U1 1/0:U1 1|0:U1 1|0:U1 0|1:U1 1/1:U1 0/0:U1 0/0:U1 0/1:U1 0|0:U1 0|0:U1 0|0:U1 1|0:U1 0/1:U1 1|1:U1 0/0:U1 0|0:U1 0/0:U1 0|0:U1 0/1:U1 0/0:U1 0/0:U1 0/1:U1 0|0:U1 0/0:U1 1/0:U1 0/0:U1 1/0:U1 0/0:U1 0/1:U1 1|0:U1 1/1:U1 1/1:U1 0/0:U1 0/0:U1 0/0:U1 1/0:U1 1|0:U1 0|1:U1 1|0:U1 1/0:U1 0|1:U1 0|1:U1 0|0:U1 0/0:U1
254
254
  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:VIPC_S 0/0:U1 0/0:U1 0/1:U1 1/0:U1 0/0:U1 1|0:U1 0/0:U1 0|0:U1 0|1:U1 0/1:U1 0/1:U1 0/0:U1 1/0:U1 0|1:U1 0/0:U1 0/1:U1 0|1:U1 1|0:U1 1/0:U1 0/1:U1 0/1:U1 1/1:U1 1/0:U1 0|0:U1 1|1:U1 1/0:U1 1|0:U1 1/0:U1 0|1:U1 1/0:U1 0/0:U1 0|1:U1 0/1:U1 0|1:U1 0/0:U1 0/1:U1 0/0:U1 1/1:U1 1/1:U1 1/0:U1 0|0:U1 0|1:U1 1/0:U1 1/0:U1 0|0:U1 0|1:U1 0|0:U1 0|0:U1 0/0:U1 1|1:U1 0|0:U1 1/0:U1 1|1:U1 1/1:U1 0/0:U1 0|1:U1 1/0:U1 0/1:U1 0|0:U1 0|0:U1 0/0:U1 0|1:U1 1|1:U1 1|1:U1 0/1:U1 1/0:U1 0|0:U1 0/0:U1 1/0:U1 0/0:U1 0/1:U1 0|1:U1 1/1:U1 0|0:U1 0|1:U1 0|1:U1 1|0:U1 0|0:U1 0|1:U1 0/0:U1 1/0:U1 1|0:U1 0/1:U1 0/1:U1 1|0:U1 1|0:U1 0/0:U1 0/0:U1 0/1:U1 0|1:U1 1|1:U1 1|1:U1 0/1:U1 1/0:U1 1/1:U1 1|0:U1 1|0:U1 0/0:U1 1|0:U1 1/0:U1
255
- 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:U1.995||pathogenic||1||||||||-27|-43|-27|-1|0:U1.00|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:U1.999||pathogenic||1||||||||-27|-43|-27|-1|0:U1.00|0.00|0.01|0.00|CLN5|VUS|0.8734921|||AR|LP|||||||P|filter&vkgl&exit_p| GT:VIPC_S 1/1:U1 0/0:U1 0/0:U1 0/1:U1 0/0:U1 0/0:U1 1|1:U1 1/0:U1 0|1:U1 1|0:U1 1|0:U1 0|1:U1 0|1:U1 1|0:U1 0/1:U1 0/1:U1 0|0:U1 1|0:U1 0|0:U1 1|0:U1 0/0:U1 1|0:U1 0|0:U1 1/1:U1 0|0:U1 0/0:U1 0/1:U1 0/0:U1 1/0:U1 1/0:U1 0|0:U1 1/1:U1 0|1:U1 0|0:U1 0|1:U1 1|0:U1 1|0:U1 1|1:U1 1|1:U1 0/1:U1 1|0:U1 1/0:U1 0|0:U1 0/1:U1 1/1:U1 0|0:U1 1/1:U1 1/0:U1 0/1:U1 0|1:U1 0/0:U1 0|0:U1 0|0:U1 0|1:U1 0|0:U1 0/1:U1 0/0:U1 0|1:U1 1/0:U1 0|1:U1 0|1:U1 1|0:U1 0/0:U1 0/1:U1 1/1:U1 0|1:U1 1|0:U1 0/0:U1 1|1:U1 0/1:U1 1|0:U1 0|0:U1 1|0:U1 0|0:U1 1/0:U1 0|0:U1 1/1:U1 0/0:U1 1/1:U1 0/1:U1 0/1:U1 0|1:U1 1|0:U1 0|1:U1 1|0:U1 0|1:U1 0/1:U1 0/0:U1 0|0:U1 1|1:U1 1/0:U1 0/1:U1 0/1:U1 0|0:U1 0/0:U1 0/1:U1 0/1:U1 0/0:U1 0|1:U1 0|0:U1
255
+ 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:VIPC_S 1/1:U1 0/0:U1 0/0:U1 0/1:U1 0/0:U1 0/0:U1 1|1:U1 1/0:U1 0|1:U1 1|0:U1 1|0:U1 0|1:U1 0|1:U1 1|0:U1 0/1:U1 0/1:U1 0|0:U1 1|0:U1 0|0:U1 1|0:U1 0/0:U1 1|0:U1 0|0:U1 1/1:U1 0|0:U1 0/0:U1 0/1:U1 0/0:U1 1/0:U1 1/0:U1 0|0:U1 1/1:U1 0|1:U1 0|0:U1 0|1:U1 1|0:U1 1|0:U1 1|1:U1 1|1:U1 0/1:U1 1|0:U1 1/0:U1 0|0:U1 0/1:U1 1/1:U1 0|0:U1 1/1:U1 1/0:U1 0/1:U1 0|1:U1 0/0:U1 0|0:U1 0|0:U1 0|1:U1 0|0:U1 0/1:U1 0/0:U1 0|1:U1 1/0:U1 0|1:U1 0|1:U1 1|0:U1 0/0:U1 0/1:U1 1/1:U1 0|1:U1 1|0:U1 0/0:U1 1|1:U1 0/1:U1 1|0:U1 0|0:U1 1|0:U1 0|0:U1 1/0:U1 0|0:U1 1/1:U1 0/0:U1 1/1:U1 0/1:U1 0/1:U1 0|1:U1 1|0:U1 0|1:U1 1|0:U1 0|1:U1 0/1:U1 0/0:U1 0|0:U1 1|1:U1 1/0:U1 0/1:U1 0/1:U1 0|0:U1 0/0:U1 0/1:U1 0/1:U1 0/0:U1 0|1:U1 0|0:U1
256
256
  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:VIPC_S 0|0:U1 0|1:U1 1|1:U1 0/0:U1 0/0:U1 0|1:U1 0|0:U1 1/0:U1 0/0:U1 1/0:U1 0/1:U1 0|1:U1 0|0:U1 1/0:U1 0|1:U1 0|0:U1 0/0:U1 0/0:U1 1|0:U1 0|0:U1 0/0:U1 0/1:U1 1|1:U1 0/0:U1 1/0:U1 0|1:U1 0/1:U1 0|0:U1 0/1:U1 1|0:U1 0/1:U1 1/0:U1 0/0:U1 1|0:U1 0|0:U1 0/0:U1 0/0:U1 1/0:U1 0|1:U1 1/1:U1 1|0:U1 0/0:U1 0|0:U1 0/1:U1 1/0:U1 1/0:U1 0/0:U1 1|0:U1 1/0:U1 0|1:U1 0/0:U1 1|0:U1 1/1:U1 1/0:U1 0|0:U1 0|1:U1 1/0:U1 0|0:U1 0/1:U1 0/0:U1 1|1:U1 1/0:U1 1/0:U1 0/0:U1 1|0:U1 0/0:U1 1/1:U1 1|1:U1 1|1:U1 1/1:U1 0|1:U1 1|0:U1 1|1:U1 0/1:U1 0|1:U1 1/1:U1 0/1:U1 1|1:U1 0|1:U1 0|1:U1 0|0:U1 1/1:U1 1|1:U1 0|1:U1 1|1:U1 0/1:U1 0|0:U1 0|0:U1 0|0:U1 1/1:U1 0|0:U1 0|1:U1 0|1:U1 0/1:U1 0|0:U1 1|1:U1 1|0:U1 0|1:U1 1/1:U1 0/1:U1
257
- 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:U1.999||||||||||||-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:U1.999||||||||||||-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:U1.999||||||||||||-28|-2|37|-2|0.00|0.00|0.00|0.00|INF2|VUS|0.89743406|||AD|LP|||||||P|filter&vkgl&exit_p| GT:VIPC_S 0|0:U1 0/0:U1 0/0:U1 1/1:U1 0/0:U1 1/1:U1 1|0:U1 1/1:U1 0/0:U1 1|0:U1 0/1:U1 0|0:U1 0/0:U1 0/0:U1 0|1:U1 0|0:U1 0/0:U1 0/0:U1 1|1:U1 0/0:U1 1/1:U1 0/1:U1 0|1:U1 1/0:U1 1|0:U1 0/1:U1 1|1:U1 0/1:U1 0/0:U1 0|1:U1 1|0:U1 0|0:U1 1|1:U1 0|1:U1 0|0:U1 0|1:U1 1/0:U1 0/1:U1 1|0:U1 1|0:U1 0|0:U1 1/0:U1 0/1:U1 0|0:U1 1/0:U1 0|1:U1 1/0:U1 0/0:U1 0|1:U1 1|1:U1 1/0:U1 0/1:U1 0/0:U1 1|0:U1 1/0:U1 0|0:U1 0/0:U1 1|1:U1 0/1:U1 1/0:U1 0/1:U1 1|0:U1 0/0:U1 1/0:U1 0/0:U1 0/1:U1 1/1:U1 1|0:U1 1/0:U1 1/1:U1 0/0:U1 0/0:U1 0|0:U1 0/1:U1 0/0:U1 1/0:U1 1/1:U1 1|1:U1 0/0:U1 1/1:U1 0/0:U1 1|0:U1 0/0:U1 1/1:U1 0/1:U1 1|0:U1 0/1:U1 0|1:U1 1/0:U1 0|1:U1 1/0:U1 0|0:U1 0|0:U1 0|0:U1 1/1:U1 0/1:U1 0/0:U1 1|1:U1 0|0:U1 0/0:U1
257
+ 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:VIPC_S 0|0:U1 0/0:U1 0/0:U1 1/1:U1 0/0:U1 1/1:U1 1|0:U1 1/1:U1 0/0:U1 1|0:U1 0/1:U1 0|0:U1 0/0:U1 0/0:U1 0|1:U1 0|0:U1 0/0:U1 0/0:U1 1|1:U1 0/0:U1 1/1:U1 0/1:U1 0|1:U1 1/0:U1 1|0:U1 0/1:U1 1|1:U1 0/1:U1 0/0:U1 0|1:U1 1|0:U1 0|0:U1 1|1:U1 0|1:U1 0|0:U1 0|1:U1 1/0:U1 0/1:U1 1|0:U1 1|0:U1 0|0:U1 1/0:U1 0/1:U1 0|0:U1 1/0:U1 0|1:U1 1/0:U1 0/0:U1 0|1:U1 1|1:U1 1/0:U1 0/1:U1 0/0:U1 1|0:U1 1/0:U1 0|0:U1 0/0:U1 1|1:U1 0/1:U1 1/0:U1 0/1:U1 1|0:U1 0/0:U1 1/0:U1 0/0:U1 0/1:U1 1/1:U1 1|0:U1 1/0:U1 1/1:U1 0/0:U1 0/0:U1 0|0:U1 0/1:U1 0/0:U1 1/0:U1 1/1:U1 1|1:U1 0/0:U1 1/1:U1 0/0:U1 1|0:U1 0/0:U1 1/1:U1 0/1:U1 1|0:U1 0/1:U1 0|1:U1 1/0:U1 0|1:U1 1/0:U1 0|0:U1 0|0:U1 0|0:U1 1/1:U1 0/1:U1 0/0:U1 1|1:U1 0|0:U1 0/0:U1
258
258
  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:VIPC_S 1/0:U1 0/1:U1 0/0:U1 1/1:U1 0/0:U1 0|1:U1 0/1:U1 1|0:U1 0|0:U1 0/1:U1 1|1:U1 0|1:U1 0|0:U1 0|0:U1 0/0:U1 0|0:U1 0/1:U1 1/0:U1 0/1:U1 0|0:U1 1/0:U1 1/0:U1 0|0:U1 1|0:U1 1/0:U1 1/1:U1 0|1:U1 0|0:U1 0/0:U1 0|1:U1 0/0:U1 1|0:U1 1|0:U1 1/1:U1 0|1:U1 1|0:U1 1|0:U1 0/0:U1 0|1:U1 1|0:U1 0/0:U1 1|1:U1 1|1:U1 1|0:U1 0|0:U1 0/1:U1 1|0:U1 0/0:U1 0|0:U1 1/0:U1 1/0:U1 0|1:U1 0/0:U1 0/1:U1 1/1:U1 1|1:U1 0|0:U1 0/1:U1 1/0:U1 0|0:U1 0|0:U1 1/1:U1 1|1:U1 1/0:U1 0/0:U1 0|0:U1 1/1:U1 1/1:U1 1/0:U1 1/0:U1 0/0:U1 0|1:U1 1/0:U1 0/0:U1 1/1:U1 1/0:U1 0|0:U1 0|1:U1 1/0:U1 1|1:U1 1|0:U1 0/1:U1 1/1:U1 0|0:U1 0|0:U1 0/0:U1 0|0:U1 0|0:U1 0/1:U1 0|0:U1 0/1:U1 0/0:U1 1|0:U1 0/1:U1 0/1:U1 0|0:U1 0|0:U1 0/0:U1 0/1:U1 0|0:U1
259
- 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:U1.994||||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:U1.993||||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:VIPC_S 0|0:U1 0/0:U1 0/0:U1 0/1:U1 0|1:U1 1/1:U1 0/0:U1 1|1:U1 1|1:U1 1|0:U1 0|0:U1 0/1:U1 1|1:U1 1/0:U1 1|1:U1 0|0:U1 0/0:U1 0/1:U1 0/1:U1 1/1:U1 1/0:U1 1/1:U1 0/0:U1 1/0:U1 0|0:U1 0|0:U1 0/1:U1 0/0:U1 0/0:U1 0/1:U1 0|0:U1 1|1:U1 0|0:U1 0/0:U1 0/0:U1 0|0:U1 1/1:U1 1/1:U1 0/0:U1 1|0:U1 0|0:U1 0|0:U1 1/1:U1 0|0:U1 1|0:U1 0/1:U1 0/0:U1 0|1:U1 1|0:U1 0/0:U1 1|1:U1 0/0:U1 1/1:U1 1/0:U1 1|0:U1 1|0:U1 1/0:U1 0|0:U1 0/1:U1 0/0:U1 1|0:U1 1/1:U1 1|1:U1 1/1:U1 1/0:U1 0|0:U1 0|0:U1 1/0:U1 1/0:U1 0|0:U1 0/0:U1 0/0:U1 0|0:U1 0/0:U1 1/0:U1 1|0:U1 1|0:U1 0|0:U1 0|1:U1 1/0:U1 0|1:U1 0|0:U1 0|0:U1 0/1:U1 1|1:U1 0/1:U1 0|0:U1 0/0:U1 0/0:U1 1/0:U1 1|0:U1 0|1:U1 0/1:U1 0|1:U1 0/0:U1 0/1:U1 0|1:U1 0|0:U1 1/1:U1 0|1:U1
259
+ 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:VIPC_S 0|0:U1 0/0:U1 0/0:U1 0/1:U1 0|1:U1 1/1:U1 0/0:U1 1|1:U1 1|1:U1 1|0:U1 0|0:U1 0/1:U1 1|1:U1 1/0:U1 1|1:U1 0|0:U1 0/0:U1 0/1:U1 0/1:U1 1/1:U1 1/0:U1 1/1:U1 0/0:U1 1/0:U1 0|0:U1 0|0:U1 0/1:U1 0/0:U1 0/0:U1 0/1:U1 0|0:U1 1|1:U1 0|0:U1 0/0:U1 0/0:U1 0|0:U1 1/1:U1 1/1:U1 0/0:U1 1|0:U1 0|0:U1 0|0:U1 1/1:U1 0|0:U1 1|0:U1 0/1:U1 0/0:U1 0|1:U1 1|0:U1 0/0:U1 1|1:U1 0/0:U1 1/1:U1 1/0:U1 1|0:U1 1|0:U1 1/0:U1 0|0:U1 0/1:U1 0/0:U1 1|0:U1 1/1:U1 1|1:U1 1/1:U1 1/0:U1 0|0:U1 0|0:U1 1/0:U1 1/0:U1 0|0:U1 0/0:U1 0/0:U1 0|0:U1 0/0:U1 1/0:U1 1|0:U1 1|0:U1 0|0:U1 0|1:U1 1/0:U1 0|1:U1 0|0:U1 0|0:U1 0/1:U1 1|1:U1 0/1:U1 0|0:U1 0/0:U1 0/0:U1 1/0:U1 1|0:U1 0|1:U1 0/1:U1 0|1:U1 0/0:U1 0/1:U1 0|1:U1 0|0:U1 1/1:U1 0|1:U1
260
260
  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:VIPC_S 0/1:U1 0/0:U1 0/1:U1 0/0:U1 0|0:U1 0/1:U1 1|0:U1 0|0:U1 1|0:U1 0/1:U1 0/1:U1 0|1:U1 1/1:U1 0/1:U1 1/0:U1 1|0:U1 0/0:U1 0/1:U1 0/0:U1 0|0:U1 0|1:U1 1|1:U1 1/1:U1 0/0:U1 1|0:U1 0|0:U1 0/0:U1 0|0:U1 0/1:U1 1|1:U1 0|1:U1 1|1:U1 1/1:U1 1|0:U1 0|0:U1 1|0:U1 0|0:U1 1/1:U1 1|0:U1 1/0:U1 0|0:U1 1|1:U1 0/0:U1 1|1:U1 0|0:U1 0/1:U1 1/0:U1 0|1:U1 1|1:U1 0/0:U1 1/0:U1 0/1:U1 1/1:U1 0|1:U1 1/0:U1 1/0:U1 0|1:U1 1/1:U1 0|0:U1 0|1:U1 0/0:U1 0/0:U1 1|1:U1 0|1:U1 1/0:U1 1|0:U1 0/0:U1 0/0:U1 1|0:U1 0/0:U1 0|0:U1 0/0:U1 0/0:U1 0/0:U1 0|0:U1 0|0:U1 1/1:U1 1|0:U1 0/0:U1 0/0:U1 1/0:U1 0/1:U1 0|1:U1 0|0:U1 1|0:U1 0/0:U1 0|1:U1 0/0:U1 0|0:U1 0/0:U1 0/1:U1 1|0:U1 0/0:U1 0|0:U1 0/0:U1 0|0:U1 0|0:U1 1|0:U1 0|0:U1 1|1:U1
261
261
  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:VIPC_S 0|1:U1 1|0:U1 0|0:U1 0/0:U1 0|0:U1 0|0:U1 0/1:U1 0/0:U1 1/1:U1 1/0:U1 1|1:U1 0/0:U1 0/0:U1 1/1:U1 1|1:U1 1/1:U1 0/1:U1 0/1:U1 1|0:U1 0/1:U1 1/0:U1 0|1:U1 0/1:U1 0|1:U1 1/0:U1 1|0:U1 0/0:U1 0|0:U1 1/0:U1 1/0:U1 0/1:U1 0|0:U1 0/1:U1 1/1:U1 0|1:U1 1/0:U1 1|0:U1 0/1:U1 1|0:U1 0|1:U1 1/1:U1 0/1:U1 0/0:U1 1|1:U1 0/1:U1 1/0:U1 1|1:U1 1/0:U1 1/0:U1 1|1:U1 0|0:U1 0/1:U1 0|1:U1 1|0:U1 0|0:U1 0/1:U1 0|1:U1 0/0:U1 0/0:U1 1|0:U1 0|0:U1 0/1:U1 1|0:U1 0|0:U1 0|0:U1 0|1:U1 1/0:U1 0|1:U1 0/0:U1 0|1:U1 1/0:U1 0/1:U1 1|1:U1 1|1:U1 1/1:U1 0/0:U1 0/1:U1 0|0:U1 0|1:U1 0|0:U1 1|0:U1 1|0:U1 1/1:U1 0/0:U1 0|1:U1 1/1:U1 1/1:U1 0|0:U1 1|1:U1 0/1:U1 0/1:U1 0|0:U1 0|1:U1 1/1:U1 0/0:U1 1/1:U1 0|0:U1 0/0:U1 0/0:U1 1/1:U1
262
262
  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:VIPC_S 0/1:U1 0|0:U1 0|1:U1 0/0:U1 1/0:U1 0|0:U1 0/0:U1 1|0:U1 0/1:U1 0/0:U1 0|0:U1 0/1:U1 0/0:U1 0|1:U1 1/0:U1 1|0:U1 0/1:U1 0|0:U1 0|0:U1 0|0:U1 1|1:U1 1|1:U1 0/0:U1 0/0:U1 0|1:U1 0|1:U1 0/0:U1 0/0:U1 0/0:U1 1/0:U1 0|0:U1 0/0:U1 0|1:U1 1/1:U1 0|1:U1 0/1:U1 0/1:U1 0|0:U1 1/1:U1 1/1:U1 0/1:U1 0/1:U1 0|0:U1 0|1:U1 0/0:U1 0/0:U1 0|0:U1 1|1:U1 1/1:U1 1|0:U1 0|0:U1 1/0:U1 1/0:U1 1|0:U1 1/1:U1 1/0:U1 1|1:U1 0|1:U1 0/0:U1 0/1:U1 1/0:U1 0/1:U1 0/0:U1 0/0:U1 1|0:U1 1/0:U1 0|0:U1 0/1:U1 0|1:U1 0/1:U1 1|0:U1 0/1:U1 0/0:U1 1|0:U1 0|1:U1 1|0:U1 0|0:U1 0|1:U1 0|1:U1 0/0:U1 0/0:U1 0|1:U1 0|0:U1 0/0:U1 0/0:U1 1/0:U1 0|1:U1 0|0:U1 0|0:U1 0|0:U1 1/1:U1 0|0:U1 0|0:U1 1|0:U1 1|1:U1 1|1:U1 0/0:U1 0|0:U1 1/1:U1 0|0:U1
263
263
  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:VIPC_S 0/0:U1 0|1:U1 0|0:U1 0/0:U1 1|1:U1 1|0:U1 1|0:U1 1/1:U1 0/0:U1 0|0:U1 0|1:U1 1|1:U1 1/1:U1 0/0:U1 0/1:U1 1/0:U1 1/1:U1 0|0:U1 0|1:U1 0/1:U1 0/0:U1 0/1:U1 0|0:U1 0/0:U1 0|1:U1 1/1:U1 1|0:U1 0|1:U1 1/0:U1 0/0:U1 1/0:U1 0|1:U1 0|1:U1 1|1:U1 0|1:U1 1|1:U1 1|0:U1 0|0:U1 0/0:U1 1/0:U1 0|0:U1 0/0:U1 0|0:U1 0/0:U1 1/0:U1 0|0:U1 1|1:U1 1|0:U1 0/0:U1 1/0:U1 0|1:U1 0/0:U1 0/1:U1 0|0:U1 0/0:U1 0|0:U1 0/0:U1 1/0:U1 1|0:U1 1|0:U1 0|0:U1 0|0:U1 0|0:U1 0|1:U1 0|1:U1 1/0:U1 0|1:U1 0/0:U1 1|0:U1 1|0:U1 0|1:U1 0/0:U1 0|1:U1 1/0:U1 1|0:U1 0|1:U1 0/0:U1 1|0:U1 0/0:U1 1/0:U1 0|1:U1 0|0:U1 1|0:U1 0|0:U1 0/1:U1 0|0:U1 0|0:U1 0/0:U1 1|1:U1 0/0:U1 0/0:U1 0|1:U1 0|1:U1 0|0:U1 1/0:U1 0/0:U1 0|0:U1 1|0:U1 1/1:U1 0|0:U1
264
- 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:U1||||||||||||-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:U1||||||||||||-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:U1||||||||||||-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:U1||||||||||||-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:U1||||||||||||-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:U1||||||||||||-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:U1||||||||||||-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:U1||||||||||||-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:U1||||||||||||-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:U1||||||||||||-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:U1||||||||||||-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:U1||||||||||||-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:U1||||||||||||-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:U1||||||||||||-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:U1||||||||||||-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:U1||||||||||||-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:U1||||||||||||-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:U1||||||||||||-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:VIPC_S 0|1:U1 0|0:U1 0|0:U1 0|1:U1 0/0:U1 0/1:U1 0|1:U1 1/0:U1 0|0:U1 0|0:U1 0|1:U1 0/0:U1 0/1:U1 0/0:U1 1|0:U1 0|0:U1 0|0:U1 1|1:U1 0|0:U1 0|0:U1 0/0:U1 1|0:U1 1|1:U1 0|1:U1 0/0:U1 1|0:U1 1/1:U1 0|0:U1 1/1:U1 1|0:U1 1/0:U1 0|0:U1 0|0:U1 1|1:U1 0/1:U1 0|0:U1 1/1:U1 0/1:U1 0/0:U1 0/0:U1 0/0:U1 0|0:U1 0/1:U1 0/1:U1 0|1:U1 1|0:U1 0|0:U1 1/0:U1 1|1:U1 0/0:U1 0/1:U1 0/1:U1 0/1:U1 0/0:U1 0/0:U1 0/0:U1 1|0:U1 1/0:U1 0|0:U1 0/1:U1 0|0:U1 0|0:U1 0/0:U1 1|1:U1 1|0:U1 0/1:U1 0/0:U1 0|0:U1 1/1:U1 0/0:U1 0|0:U1 0/1:U1 0/0:U1 0|1:U1 1/1:U1 0/1:U1 1|1:U1 0|0:U1 1/1:U1 1/0:U1 1|1:U1 0|1:U1 1|1:U1 0|0:U1 1|1:U1 0/0:U1 1|0:U1 0|1:U1 1/0:U1 0/1:U1 1|0:U1 0/0:U1 0|1:U1 0/1:U1 0|0:U1 0|1:U1 1/0:U1 0|0:U1 1|1:U1 0/1:U1
264
+ 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|0.001||||||||||||-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|0.001||||||||||||-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|0.001||||||||||||-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|0.001||||||||||||-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|0.001||||||||||||-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|0.001||||||||||||-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|0.001||||||||||||-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|0.001||||||||||||-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|0.001||||||||||||-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|0.001||||||||||||-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|0.001||||||||||||-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|0.001||||||||||||-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|0.001||||||||||||-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|0.001||||||||||||-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|0.001||||||||||||-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|0.001||||||||||||-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|0.001||||||||||||-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|0.001||||||||||||-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:VIPC_S 0|1:U1 0|0:U1 0|0:U1 0|1:U1 0/0:U1 0/1:U1 0|1:U1 1/0:U1 0|0:U1 0|0:U1 0|1:U1 0/0:U1 0/1:U1 0/0:U1 1|0:U1 0|0:U1 0|0:U1 1|1:U1 0|0:U1 0|0:U1 0/0:U1 1|0:U1 1|1:U1 0|1:U1 0/0:U1 1|0:U1 1/1:U1 0|0:U1 1/1:U1 1|0:U1 1/0:U1 0|0:U1 0|0:U1 1|1:U1 0/1:U1 0|0:U1 1/1:U1 0/1:U1 0/0:U1 0/0:U1 0/0:U1 0|0:U1 0/1:U1 0/1:U1 0|1:U1 1|0:U1 0|0:U1 1/0:U1 1|1:U1 0/0:U1 0/1:U1 0/1:U1 0/1:U1 0/0:U1 0/0:U1 0/0:U1 1|0:U1 1/0:U1 0|0:U1 0/1:U1 0|0:U1 0|0:U1 0/0:U1 1|1:U1 1|0:U1 0/1:U1 0/0:U1 0|0:U1 1/1:U1 0/0:U1 0|0:U1 0/1:U1 0/0:U1 0|1:U1 1/1:U1 0/1:U1 1|1:U1 0|0:U1 1/1:U1 1/0:U1 1|1:U1 0|1:U1 1|1:U1 0|0:U1 1|1:U1 0/0:U1 1|0:U1 0|1:U1 1/0:U1 0/1:U1 1|0:U1 0/0:U1 0|1:U1 0/1:U1 0|0:U1 0|1:U1 1/0:U1 0|0:U1 1|1:U1 0/1:U1
265
265
  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:VIPC_S 0/0:U1 1|0:U1 0/0:U1 0/1:U1 0/1:U1 0|0:U1 0|1:U1 0|1:U1 1|0:U1 0|0:U1 1|1:U1 0/0:U1 1/0:U1 0|0:U1 1/0:U1 0|0:U1 1/0:U1 0|1:U1 0/0:U1 1|0:U1 1/0:U1 0/1:U1 0|1:U1 1|0:U1 1|1:U1 1|0:U1 0/0:U1 0|0:U1 0/0:U1 0/0:U1 0|1:U1 1|0:U1 0|0:U1 0|0:U1 1|0:U1 0|0:U1 0/0:U1 1|0:U1 1/0:U1 1/0:U1 0/0:U1 1|0:U1 0/0:U1 0/0:U1 1|1:U1 1|1:U1 0|0:U1 0|0:U1 1|0:U1 0|1:U1 1/0:U1 0/0:U1 0|0:U1 1/0:U1 0|0:U1 1/0:U1 1/0:U1 0|0:U1 0/0:U1 0|0:U1 1/0:U1 1|1:U1 1/1:U1 0|1:U1 0/1:U1 0|0:U1 1/1:U1 0|1:U1 0/0:U1 1|0:U1 0/1:U1 1|0:U1 0|0:U1 0|0:U1 0|1:U1 0/0:U1 0/1:U1 0/0:U1 0/0:U1 0/1:U1 1|0:U1 0|1:U1 0|0:U1 0/0:U1 1/0:U1 0|0:U1 0|0:U1 0|1:U1 0|1:U1 1/0:U1 0/0:U1 0/1:U1 0/0:U1 0/0:U1 1/0:U1 1|1:U1 1|0:U1 1|1:U1 1|1:U1 0/0:U1
266
266
  chrY 2787600 y_chrom G A . PASS CSQ=A|stop_gained|HIGH|SRY|6736|Transcript|NM_003140.3|protein_coding|1/1:U1||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:VIPC_S 0/1:U1 1|0:U1 1/1:U1 1|0:U1 0/1:U1 1|0:U1 0|0:U1 0/1:U1 1/0:U1 0/1:U1 0/0:U1 0|1:U1 1|1:U1 0/0:U1 1/0:U1 1/0:U1 1/0:U1 0/0:U1 1|1:U1 1|0:U1 0/1:U1 0/1:U1 0/0:U1 1/1:U1 1|0:U1 1/0:U1 0|1:U1 1/0:U1 0|0:U1 1|0:U1 1/0:U1 0/0:U1 0/0:U1 1/0:U1 0/0:U1 0/0:U1 0/0:U1 1/0:U1 0/0:U1 1|0:U1 0|1:U1 0|0:U1 0|1:U1 0|0:U1 1|0:U1 1/1:U1 0|1:U1 1|1:U1 0/1:U1 1/1:U1 1|0:U1 0/1:U1 1/0:U1 1|0:U1 1/0:U1 1/0:U1 0/1:U1 1/0:U1 0|0:U1 0/0:U1 0|0:U1 0/1:U1 1/1:U1 0|0:U1 0/0:U1 1|0:U1 1|1:U1 0/1:U1 0|0:U1 0/0:U1 0/0:U1 0|1:U1 1/0:U1 0|0:U1 0|0:U1 0|0:U1 1|1:U1 1|0:U1 0/1:U1 0|1:U1 0|0:U1 1/0:U1 0/0:U1 1/0:U1 1|1:U1 1|0:U1 0|1:U1 0/0:U1 1/1:U1 1|0:U1 0|0:U1 0|0:U1 0/0:U1 0/0:U1 0|1:U1 0|0:U1 0|1:U1 0/1:U1 0|0:U1 0|0:U1
267
267
  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:VIPC_S 1/1:U1 1|1:U1 1|1:U1 0|0:U1 1/0:U1 0/0:U1 1/0:U1 0|0:U1 1|0:U1 1|0:U1 1/0:U1 0/1:U1 0/1:U1 0/1:U1 1/1:U1 0/1:U1 0/1:U1 0/1:U1 1|1:U1 1|0:U1 0|0:U1 0/0:U1 0|0:U1 1/1:U1 1|1:U1 0/0:U1 0|1:U1 1|0:U1 0|0:U1 1|0:U1 1|0:U1 0|0:U1 0|0:U1 0/1:U1 1|1:U1 0/1:U1 0/1:U1 1|1:U1 1|0:U1 0|0:U1 0|0:U1 0/0:U1 1|0:U1 0/0:U1 1|0:U1 1/0:U1 1|0:U1 1/0:U1 0/1:U1 0|1:U1 1/0:U1 1/0:U1 1/1:U1 0/1:U1 0|0:U1 0|1:U1 1|0:U1 0|1:U1 0|0:U1 1|1:U1 0/0:U1 1|1:U1 0/0:U1 0|1:U1 0|0:U1 0/0:U1 0|0:U1 0/1:U1 1|0:U1 0|0:U1 0|0:U1 0|0:U1 0/0:U1 1|0:U1 0/0:U1 1|0:U1 0/0:U1 1/1:U1 1|1:U1 0|0:U1 1/0:U1 0|1:U1 0|0:U1 0|0:U1 0|0:U1 1|0:U1 0|0:U1 0/1:U1 0/1:U1 0|1:U1 0|0:U1 1/0:U1 1/1:U1 0/0:U1 1|0:U1 1|0:U1 1|0:U1 1/0:U1 1/1:U1 0|0:U1
package/src/mocks/GRCh38/vcf/str.db.blob ADDED
Binary file
package/src/mocks/GRCh38/vcf/{str.vcf.blob → str.vcf} RENAMED
@@ -290,32 +290,32 @@
290
290
  ##VIP_Version=7.9.0
291
291
  ##VIP_Command=nextflow -C <PATH>/vip/v7.9.0/config/nxf_fastq.config,<PATH>/resources/run_v1.0.0.cfg -log <PATH>/<removed>/run01/results/.nxf.log run <PATH>/vip/v7.9.0/vip_fastq.nf -offline -profile slurm -with-report <PATH>/<removed>/run01/results/nxf_report.html -with-timeline <PATH>/<removed>/run01/results/nxf_timeline.html --input <PATH>/<removed>/run01/vip/sample_sheet.tsv --output <PATH>/<removed>/run01/results
292
292
  #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Patient
293
- chr1 149390803 . G <CNV:TR>,<CNV:TR> . PASS CSQ=tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|NOTCH2NLC|100996717|Transcript|NM_001364013.2|protein_coding|1/5||||184-221/8729|17-54/882|6-18/293||||1||1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||LB|type&pick&gene_str&up_downstream&unit&status&exit_lb;Disease=NIID/OPDM3;DisplayRU=CGG;END=149390841;HGNCId=53924;REF=13;REPID=NOTCH2NLC;RL=39;RU=GGC;RUMATCH;RankScore=1:10;STR_NORMAL_MAX=60;STR_PATHOLOGIC_MIN=61;STR_STATUS=normal,normal;SVTYPE=STR;VARID=NOTCH2NLC;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/2:0/0:0/0:14/28:34:18-18/7-17:18/13:SPANNING/SPANNING:AR,AD::.:100996717:1:U1:gt&gq&only_IP&vim&exit_u1
294
- chr12 6936717 . C <CNV:TR>,<CNV:TR> . PASS CSQ=tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|ATN1|1822|Transcript|NM_001940.4|protein_coding|5/10||||2039-2094/4702|1451-1506/3573|484-502/1190||||1||1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||LB|type&pick&gene_str&up_downstream&unit&status&exit_lb;Disease=DRPLA;DisplayRU=CAG;END=6936773;HGNCId=3033;REF=19;REPID=ATN1;RL=57;RU=CAG;RUMATCH;RankScore=1:10;STR_NORMAL_MAX=35;STR_PATHOLOGIC_MIN=48;STR_STATUS=normal,normal;SVTYPE=STR;VARID=ATN1;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/2:0/0:0/0:27/8:38:19-20/15-18:19/17:SPANNING/SPANNING:AR,AD::.:1822:1:U1:gt&gq&only_IP&vim&exit_u1
293
+ chr1 149390803 . G <CNV:TR1>,<CNV:TR2> . PASS CSQ=tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|NOTCH2NLC|100996717|Transcript|NM_001364013.2|protein_coding|1/5||||184-221/8729|17-54/882|6-18/293||||1||1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||LB|type&pick&gene_str&up_downstream&unit&status&exit_lb;Disease=NIID/OPDM3;DisplayRU=CGG;END=149390841;HGNCId=53924;REF=13;REPID=NOTCH2NLC;RL=39;RUMATCH;RankScore=1:10;STR_NORMAL_MAX=60;STR_PATHOLOGIC_MIN=61;STR_STATUS=normal,normal;SVTYPE=STR;VARID=NOTCH2NLC;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/2:0/0:0/0:14/28:34:18-18/7-17:18/13:SPANNING/SPANNING:AR,AD::.:100996717:1:U1:gt&gq&only_IP&vim&exit_u1
294
+ chr12 6936717 . C <CNV:TR1>,<CNV:TR2> . PASS CSQ=tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|ATN1|1822|Transcript|NM_001940.4|protein_coding|5/10||||2039-2094/4702|1451-1506/3573|484-502/1190||||1||1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||LB|type&pick&gene_str&up_downstream&unit&status&exit_lb;Disease=DRPLA;DisplayRU=CAG;END=6936773;HGNCId=3033;REF=19;REPID=ATN1;RL=57;RU=CAG;RUMATCH;RankScore=1:10;STR_NORMAL_MAX=35;STR_PATHOLOGIC_MIN=48;STR_STATUS=normal,normal;SVTYPE=STR;VARID=ATN1;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/2:0/0:0/0:27/8:38:19-20/15-18:SPANNING/SPANNING:AR,AD::.:1822:1:U1:gt&gq&only_IP&vim&exit_u1
295
295
  chr12 111598950 . G <CNV:TR> . PASS CSQ=tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|ATXN2|6311|Transcript|NM_001372574.1|protein_coding|1/25||||298-365/4347|17-84/3468|6-28/1155||||1||-1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||LB|type&pick&gene_str&up_downstream&unit&status&exit_lb;Disease=SCA2;DisplayRU=CTG;END=111599018;HGNCId=10555;REF=23;REPID=ATXN2;RL=69;RU=GCT;RUMATCH;RankScore=1:10;STR_NORMAL_MAX=31;STR_PATHOLOGIC_MIN=32;STR_STATUS=normal;SVTYPE=STR;VARID=ATXN2;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/1:0/0:0/0:16.0/16.0:32:21-23/21-23:22/22:SPANNING/SPANNING:AR,AD::.:6311:1:U1:gt&gq&only_IP&vim&exit_u1
296
296
  chr13 70139384 . C <CNV:TR> . PASS CSQ=tandem_duplication|feature_elongation&non_coding_transcript_exon_variant|HIGH|ATXN8OS|6315|Transcript|NR_002717.2|antisense_RNA|5/5||||1104-1147/1472||||||1||1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||VUS|type&pick&gene_str&up_downstream&unit&status&exit_vus;END=70139428;REF=15;REPID=ATXN8;RL=45;RU=CTG;RUMATCH;SVTYPE=STR;VARID=ATXN8;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/1:0/0:0/0:21.5/21.5:45:15-16/15-16:16/16:SPANNING/SPANNING:AR,AD::.:6315:1:U1:gt&gq&only_IP&vim&exit_u1
297
- chr13 102161577 . G <CNV:TR>,<CNV:TR> . PASS CSQ=tandem_duplication|feature_elongation&intron_variant|HIGH|FGF14|2259|Transcript|NM_175929.3|protein_coding||1/4|||||||||1||-1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||LB|type&pick&gene_str&up_downstream&unit&status&exit_lb;Disease=SCA27B;DisplayRU=GAA;END=102161726;HGNCId=3671;REF=50;REPID=FGF14;RL=150;RU=AAG;RUMATCH;RankScore=1:10;STR_NORMAL_MAX=249;STR_PATHOLOGIC_MIN=250;STR_STATUS=normal,normal;SVTYPE=STR;VARID=FGF14;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/2:0/0:0/0:13/19:34:15-17/9-11:16/10:SPANNING/SPANNING:AR,AD::.:2259:1:U1:gt&gq&only_IP&vim&exit_u1
297
+ chr13 102161577 . G <CNV:TR1>,<CNV:TR2> . PASS CSQ=tandem_duplication|feature_elongation&intron_variant|HIGH|FGF14|2259|Transcript|NM_175929.3|protein_coding||1/4|||||||||1||-1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||LB|type&pick&gene_str&up_downstream&unit&status&exit_lb;Disease=SCA27B;DisplayRU=GAA;END=102161726;HGNCId=3671;REF=50;REPID=FGF14;RL=150;RU=AAG;RUMATCH;RankScore=1:10;STR_NORMAL_MAX=249;STR_PATHOLOGIC_MIN=250;STR_STATUS=normal,normal;SVTYPE=STR;VARID=FGF14;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/2:0/0:0/0:13/19:34:15-17/9-11:16/10:SPANNING/SPANNING:AR,AD::.:2259:1:U1:gt&gq&only_IP&vim&exit_u1
298
298
  chr14 92071010 . C <CNV:TR> . PASS CSQ=tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|ATXN3|4287|Transcript|NM_004993.6|protein_coding|10/11||||914-945/6884|884-915/1086|295-305/361||||1||-1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||LB|type&pick&gene_str&up_downstream&unit&status&exit_lb;Disease=SCA3;DisplayRU=CTG;END=92071042;HGNCId=7106;REF=11;REPID=ATXN3;RL=33;RU=CTG;RUMATCH;RankScore=1:10;STR_NORMAL_MAX=44;STR_PATHOLOGIC_MIN=55;STR_STATUS=normal;SVTYPE=STR;VARID=ATXN3;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/1:0/0:0/0:18.0/18.0:39:19-21/19-21:20/20:SPANNING/SPANNING:AR,AD::.:4287:1:U1:gt&gq&only_IP&vim&exit_u1
299
- chr16 17470909 . C <CNV:TR>,<CNV:TR> . PASS CSQ=tandem_duplication|feature_elongation&5_prime_UTR_variant|HIGH|XYLT1|64131|Transcript|NM_022166.4|protein_coding|1/12||||40-51/9970||||||1||-1||1|EntrezGene||||||||||||||||||||||||||||||||||||AR||||||||||||||||||||||VUS|type&pick&gene_str&up_downstream&unit&exit_vus;Disease=BSS;DisplayRU=GCC;END=17470921;HGNCId=15516;REF=1;REPID=XYLT1;RL=13;RU=GCCGCCGCC;RankScore=1:20;STR_NORMAL_MAX=20;STR_PATHOLOGIC_MIN=120;STR_STATUS=pre_mutation,normal;SVTYPE=STR;VARID=XYLT1;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/2:0/0:0/0:12/13:33:22-23/16-20:22/18:SPANNING/SPANNING:AR,AD::.:64131:1:U1:gt&gq&only_IP&vim&exit_u1
299
+ chr16 17470909 . C <CNV:TR1>,<CNV:TR2> . PASS CSQ=tandem_duplication|feature_elongation&5_prime_UTR_variant|HIGH|XYLT1|64131|Transcript|NM_022166.4|protein_coding|1/12||||40-51/9970||||||1||-1||1|EntrezGene||||||||||||||||||||||||||||||||||||AR||||||||||||||||||||||VUS|type&pick&gene_str&up_downstream&unit&exit_vus;Disease=BSS;DisplayRU=GCC;END=17470921;HGNCId=15516;REF=1;REPID=XYLT1;RL=13;RU=GCCGCCGCC;RankScore=1:20;STR_NORMAL_MAX=20;STR_PATHOLOGIC_MIN=120;STR_STATUS=pre_mutation,normal;SVTYPE=STR;VARID=XYLT1;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/2:0/0:0/0:12/13:33:22-23/16-20:22/18:SPANNING/SPANNING:AR,AD::.:64131:1:U1:gt&gq&only_IP&vim&exit_u1
300
300
  chr16 87604288 . C <CNV:TR> . PASS CSQ=tandem_duplication|feature_elongation&intron_variant|HIGH|JPH3|57338|Transcript|NM_020655.4|protein_coding||1/4|||||||||1||1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||LB|type&pick&gene_str&up_downstream&unit&status&exit_lb;Disease=HDL2;DisplayRU=CTG;END=87604329;HGNCId=14203;REF=14;REPID=JPH3;RL=42;RU=GCT;RUMATCH;RankScore=1:10;STR_NORMAL_MAX=28;STR_PATHOLOGIC_MIN=41;STR_STATUS=normal;SVTYPE=STR;VARID=JPH3;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/1:0/0:0/0:20.5/20.5:44:15-16/15-16:16/16:SPANNING/SPANNING:AR,AD::.:57338:1:U1:gt&gq&only_IP&vim&exit_u1
301
- chr18 55586156 . C <CNV:TR>,<CNV:TR> . PASS CSQ=tandem_duplication|feature_elongation&intron_variant|HIGH|TCF4|6925|Transcript|NM_001083962.2|protein_coding||2/19|||||||||1||-1||1|EntrezGene|||||||||||||||||||||||||||||||||||1|AD||||||||||||||||||||||LB|type&pick&gene_str&up_downstream&unit&status&exit_lb;Disease=FECD;DisplayRU=GCA;END=55586227;HGNCId=11634;REF=24;REPID=TCF4;RL=72;RU=AGC;RUMATCH;RankScore=1:10;STR_NORMAL_MAX=31;STR_PATHOLOGIC_MIN=50;STR_STATUS=normal,normal;SVTYPE=STR;VARID=TCF4;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/2:0/0:0/0:25/22:51:26-28/16-18:27/17:SPANNING/SPANNING:AR,AD::.:6925:1:U1:gt&gq&only_IP&vim&exit_u1
302
- chr19 13207859 . C <CNV:TR>,<CNV:TR> . PASS CSQ=tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|CACNA1A|773|Transcript|NM_001127222.2|protein_coding|47/47||||7192-7229/8647|6937-6974/7521|2313-2325/2506||||1||-1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||LB|type&pick&gene_str&up_downstream&unit&status&exit_lb;Disease=SCA6;DisplayRU=CTG;END=13207897;HGNCId=1388;REF=13;REPID=CACNA1A;RL=39;RU=CTG;RUMATCH;RankScore=1:10;STR_NORMAL_MAX=18;STR_PATHOLOGIC_MIN=20;STR_STATUS=normal,normal;SVTYPE=STR;VARID=CACNA1A;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/2:0/0:0/0:33/2:39:11-12/6-8:11/7:SPANNING/SPANNING:AR,AD::.:773:1:U1:gt&gq&only_IP&vim&exit_u1
303
- chr19 14496043 . C <CNV:TR>,<CNV:TR> . PASS CSQ=tandem_duplication|feature_elongation&5_prime_UTR_variant|HIGH|GIPC1|10755|Transcript|NM_005716.4|protein_coding|1/9||||54-84/1921||||||1||-1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||VUS|type&pick&gene_str&up_downstream&unit&exit_vus;Disease=OPDM2;DisplayRU=CCG;END=14496074;HGNCId=1226;REF=5;REPID=GIPC1;RL=32;RU=CTCCGC;RankScore=1:10;STR_NORMAL_MAX=32;STR_PATHOLOGIC_MIN=97;STR_STATUS=normal,normal;SVTYPE=STR;VARID=GIPC1;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/2:0/0:0/0:8/27:40:7-8/5-6:7/6:SPANNING/SPANNING:AR,AD::.:10755:1:U1:gt&gq&only_IP&vim&exit_u1
304
- chr19 45770205 . C <CNV:TR>,<CNV:TR> . PASS CSQ=tandem_duplication|feature_elongation&3_prime_UTR_variant|HIGH|DMPK|1760|Transcript|NM_004409.5|protein_coding|15/15||||2252-2310/2799||||||1||-1||1|EntrezGene|||||||||||||||||||||||||||||||||||1|AD&AR||||||||||||||||||||||LB|type&pick&gene_str&up_downstream&unit&status&exit_lb;Disease=DM1;DisplayRU=CAG;END=45770264;HGNCId=2933;REF=20;REPID=DMPK;RL=60;RU=CAG;RUMATCH;RankScore=1:10;STR_NORMAL_MAX=37;STR_PATHOLOGIC_MIN=50;STR_STATUS=normal,normal;SVTYPE=STR;VARID=DMPK;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/2:0/0:0/0:30/16:48:13-14/6-6:14/6:SPANNING/SPANNING:AR,AD::.:1760:1:U1:gt&gq&only_IP&vim&exit_u1
301
+ chr18 55586156 . C <CNV:TR1>,<CNV:TR2> . PASS CSQ=tandem_duplication|feature_elongation&intron_variant|HIGH|TCF4|6925|Transcript|NM_001083962.2|protein_coding||2/19|||||||||1||-1||1|EntrezGene|||||||||||||||||||||||||||||||||||1|AD||||||||||||||||||||||LB|type&pick&gene_str&up_downstream&unit&status&exit_lb;Disease=FECD;DisplayRU=GCA;END=55586227;HGNCId=11634;REF=24;REPID=TCF4;RL=72;RU=AGC;RUMATCH;RankScore=1:10;STR_NORMAL_MAX=31;STR_PATHOLOGIC_MIN=50;STR_STATUS=normal,normal;SVTYPE=STR;VARID=TCF4;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/2:0/0:0/0:25/22:51:26-28/16-18:27/17:SPANNING/SPANNING:AR,AD::.:6925:1:U1:gt&gq&only_IP&vim&exit_u1
302
+ chr19 13207859 . C <CNV:TR1>,<CNV:TR2> . PASS CSQ=tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|CACNA1A|773|Transcript|NM_001127222.2|protein_coding|47/47||||7192-7229/8647|6937-6974/7521|2313-2325/2506||||1||-1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||LB|type&pick&gene_str&up_downstream&unit&status&exit_lb;Disease=SCA6;DisplayRU=CTG;END=13207897;HGNCId=1388;REF=13;REPID=CACNA1A;RL=39;RU=CTG;RUMATCH;RankScore=1:10;STR_NORMAL_MAX=18;STR_PATHOLOGIC_MIN=20;STR_STATUS=normal,normal;SVTYPE=STR;VARID=CACNA1A;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/2:0/0:0/0:33/2:39:11-12/6-8:11/7:SPANNING/SPANNING:AR,AD::.:773:1:U1:gt&gq&only_IP&vim&exit_u1
303
+ chr19 14496043 . C <CNV:TR1>,<CNV:TR2> . PASS CSQ=tandem_duplication|feature_elongation&5_prime_UTR_variant|HIGH|GIPC1|10755|Transcript|NM_005716.4|protein_coding|1/9||||54-84/1921||||||1||-1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||VUS|type&pick&gene_str&up_downstream&unit&exit_vus;Disease=OPDM2;DisplayRU=CCG;END=14496074;HGNCId=1226;REF=5;REPID=GIPC1;RL=32;RU=CTCCGC;RankScore=1:10;STR_NORMAL_MAX=32;STR_PATHOLOGIC_MIN=97;STR_STATUS=normal,normal;SVTYPE=STR;VARID=GIPC1;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/2:0/0:0/0:8/27:40:7-8/5-6:7/6:SPANNING/SPANNING:AR,AD::.:10755:1:U1:gt&gq&only_IP&vim&exit_u1
304
+ chr19 45770205 . C <CNV:TR1>,<CNV:TR2> . PASS CSQ=tandem_duplication|feature_elongation&3_prime_UTR_variant|HIGH|DMPK|1760|Transcript|NM_004409.5|protein_coding|15/15||||2252-2310/2799||||||1||-1||1|EntrezGene|||||||||||||||||||||||||||||||||||1|AD&AR||||||||||||||||||||||LB|type&pick&gene_str&up_downstream&unit&status&exit_lb;Disease=DM1;DisplayRU=CAG;END=45770264;HGNCId=2933;REF=20;REPID=DMPK;RL=60;RU=CAG;RUMATCH;RankScore=1:10;STR_NORMAL_MAX=37;STR_PATHOLOGIC_MIN=50;STR_STATUS=normal,normal;SVTYPE=STR;VARID=DMPK;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/2:0/0:0/0:30/16:48:13-14/6-6:14/6:SPANNING/SPANNING:AR,AD::.:1760:1:U1:gt&gq&only_IP&vim&exit_u1
305
305
  chr2 176093060 . C <CNV:TR> . PASS CSQ=tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|HOXD13|3239|Transcript|NM_000523.4|protein_coding|1/2||||341-383/2416|171-213/1032|57-71/343||||1||1||1|EntrezGene|||||||||||||||||||||||||||||||||||1|AD&AR||||||||||||||||||||||VUS|type&pick&gene_str&up_downstream&unit&status&exit_vus;Disease=SPD1;DisplayRU=GCG;END=176093103;HGNCId=5136;REF=14;REPID=HOXD13;RL=44;RU=CGG;RUMATCH;RankScore=1:20;STR_NORMAL_MAX=15;STR_PATHOLOGIC_MIN=24;STR_STATUS=pre_mutation;SVTYPE=STR;VARID=HOXD13;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/1:0/0:0/0:21.5/21.5:45:15-16/15-16:16/16:SPANNING/SPANNING:AR,AD::.:3239:1:U1:gt&gq&only_IP&vim&exit_u1
306
- chr2 190880873 . G <CNV:TR>,<CNV:TR> . PASS CSQ=tandem_duplication|feature_elongation&5_prime_UTR_variant|HIGH|GLS|2744|Transcript|NM_014905.5|protein_coding|1/18||||54-100/4840||||||1||1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||||||||||LB|type&pick&gene_str&up_downstream&unit&status&exit_lb;Disease=GDPAG;DisplayRU=GCA;END=190880920;HGNCId=4331;REF=16;REPID=GLS;RL=48;RU=GCA;RUMATCH;RankScore=1:10;STR_NORMAL_MAX=16;STR_PATHOLOGIC_MIN=680;STR_STATUS=normal,normal;SVTYPE=STR;VARID=GLS;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/2:0/0:0/0:36/2:42:12-14/7-8:13/7:SPANNING/SPANNING:AR,AD::.:2744:1:U1:gt&gq&only_IP&vim&exit_u1
307
- chr20 2652734 . G <CNV:TR>,<CNV:TR> . PASS CSQ=tandem_duplication|feature_elongation&intron_variant|HIGH|NOP56|10528|Transcript|NM_006392.4|protein_coding||1/11|||||||||1||1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||LB|type&pick&gene_str&up_downstream&unit&status&exit_lb;Disease=SCA36;DisplayRU=GGCCTG;END=2652757;HGNCId=15911;REF=4;REPID=NOP56;RL=24;RU=GGGCCT;RUMATCH;RankScore=1:10;STR_NORMAL_MAX=14;STR_PATHOLOGIC_MIN=650;STR_STATUS=normal,normal;SVTYPE=STR;VARID=NOP56;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/2:0/0:0/0:23/2:27:7-8/5-5:7/5:SPANNING/SPANNING:AR,AD::.:10528:1:U1:gt&gq&only_IP&vim&exit_u1
308
- chr22 45795355 . A <CNV:TR>,<CNV:TR> . PASS CSQ=tandem_duplication|feature_elongation&intron_variant|HIGH|ATXN10|25814|Transcript|NM_013236.4|protein_coding||9/11|||||||||1||1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||LB|type&pick&gene_str&up_downstream&unit&status&exit_lb;Disease=SCA10;DisplayRU=ATTCT;END=45795424;HGNCId=10549;REF=14;REPID=ATXN10;RL=70;RU=ATTCT;RUMATCH;RankScore=1:10;STR_NORMAL_MAX=32;STR_PATHOLOGIC_MIN=280;STR_STATUS=normal,normal;SVTYPE=STR;VARID=ATXN10;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/2:0/0:0/0:16/20:42:16-16/13-13:16/13:SPANNING/SPANNING:AR,AD::.:25814:1:U1:gt&gq&only_IP&vim&exit_u1
306
+ chr2 190880873 . G <CNV:TR1>,<CNV:TR2> . PASS CSQ=tandem_duplication|feature_elongation&5_prime_UTR_variant|HIGH|GLS|2744|Transcript|NM_014905.5|protein_coding|1/18||||54-100/4840||||||1||1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD&AR||||||||||||||||||||||LB|type&pick&gene_str&up_downstream&unit&status&exit_lb;Disease=GDPAG;DisplayRU=GCA;END=190880920;HGNCId=4331;REF=16;REPID=GLS;RL=48;RU=GCA;RUMATCH;RankScore=1:10;STR_NORMAL_MAX=16;STR_PATHOLOGIC_MIN=680;STR_STATUS=normal,normal;SVTYPE=STR;VARID=GLS;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/2:0/0:0/0:36/2:42:12-14/7-8:13/7:SPANNING/SPANNING:AR,AD::.:2744:1:U1:gt&gq&only_IP&vim&exit_u1
307
+ chr20 2652734 . G <CNV:TR1>,<CNV:TR2> . PASS CSQ=tandem_duplication|feature_elongation&intron_variant|HIGH|NOP56|10528|Transcript|NM_006392.4|protein_coding||1/11|||||||||1||1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||LB|type&pick&gene_str&up_downstream&unit&status&exit_lb;Disease=SCA36;DisplayRU=GGCCTG;END=2652757;HGNCId=15911;REF=4;REPID=NOP56;RL=24;RU=GGGCCT;RUMATCH;RankScore=1:10;STR_NORMAL_MAX=14;STR_PATHOLOGIC_MIN=650;STR_STATUS=normal,normal;SVTYPE=STR;VARID=NOP56;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/2:0/0:0/0:23/2:27:7-8/5-5:7/5:SPANNING/SPANNING:AR,AD::.:10528:1:U1:gt&gq&only_IP&vim&exit_u1
308
+ chr22 45795355 . A <CNV:TR1>,<CNV:TR2> . PASS CSQ=tandem_duplication|feature_elongation&intron_variant|HIGH|ATXN10|25814|Transcript|NM_013236.4|protein_coding||9/11|||||||||1||1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||LB|type&pick&gene_str&up_downstream&unit&status&exit_lb;Disease=SCA10;DisplayRU=ATTCT;END=45795424;HGNCId=10549;REF=14;REPID=ATXN10;RL=70;RU=ATTCT;RUMATCH;RankScore=1:10;STR_NORMAL_MAX=32;STR_PATHOLOGIC_MIN=280;STR_STATUS=normal,normal;SVTYPE=STR;VARID=ATXN10;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/2:0/0:0/0:16/20:42:16-16/13-13:16/13:SPANNING/SPANNING:AR,AD::.:25814:1:U1:gt&gq&only_IP&vim&exit_u1
309
309
  chr3 63912686 . C <CNV:TR> . PASS CSQ=tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|ATXN7|6314|Transcript|NM_001377405.1|protein_coding|3/13||||491-519/7076|89-117/2679|30-39/892||||1||1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||LB|type&pick&gene_str&up_downstream&unit&status&exit_lb;Disease=SCA7;DisplayRU=CAG;END=63912715;HGNCId=10560;REF=10;REPID=ATXN7;RL=30;RU=GCA;RUMATCH;RankScore=1:10;STR_NORMAL_MAX=19;STR_PATHOLOGIC_MIN=36;STR_STATUS=normal;SVTYPE=STR;VARID=ATXN7;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/1:0/0:0/0:14.5/14.5:31:9-12/9-12:11/11:SPANNING/SPANNING:AR,AD::.:6314:1:U1:gt&gq&only_IP&vim&exit_u1
310
310
  chr3 129172577 . C <CNV:TR> . PASS CSQ=tandem_duplication|feature_elongation&intron_variant|HIGH|CNBP|7555|Transcript|NM_003418.5|protein_coding||1/4|||||||||1||-1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||VUS|type&pick&gene_str&up_downstream&unit&exit_vus;Disease=DM2;DisplayRU=CAGG;END=129172656;HGNCId=13164;REF=10;REPID=CNBP;RL=80;RU=CAGACAGG;RankScore=1:10;STR_NORMAL_MAX=30;STR_PATHOLOGIC_MIN=50;STR_STATUS=normal;SVTYPE=STR;VARID=CNBP;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/1:0/0:0/0:9.0/9.0:39:6-8/6-8:7/7:SPANNING/SPANNING:AR,AD::.:7555:1:U1:gt&gq&only_IP&vim&exit_u1
311
- chr4 39348425 . A <CNV:TR>,<CNV:TR> . PASS CSQ=tandem_duplication|feature_elongation&intron_variant|HIGH|RFC1|5981|Transcript|NM_002913.5|protein_coding||2/24|||||||||1||-1||1|EntrezGene||||||||||||||||||||||||||||||||||||AR||||||||||||||||||||||LB|type&pick&gene_str&up_downstream&unit&status&exit_lb;Disease=CANVAS;DisplayRU=ANNNN;END=39348485;HGNCId=9969;REF=12;REPID=RFC1;RL=61;RU=AAAAG;RUMATCH;RankScore=1:10;STR_NORMAL_MAX=15;STR_PATHOLOGIC_MIN=300;STR_STATUS=normal,normal;SVTYPE=STR;VARID=RFC1;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/2:0/0:0/0:29/19:51:12-13/9-9:13/9:SPANNING/SPANNING:AR,AD::.:5981:1:U1:gt&gq&only_IP&vim&exit_u1
311
+ chr4 39348425 . A <CNV:TR1>,<CNV:TR2> . PASS CSQ=tandem_duplication|feature_elongation&intron_variant|HIGH|RFC1|5981|Transcript|NM_002913.5|protein_coding||2/24|||||||||1||-1||1|EntrezGene||||||||||||||||||||||||||||||||||||AR||||||||||||||||||||||LB|type&pick&gene_str&up_downstream&unit&status&exit_lb;Disease=CANVAS;DisplayRU=ANNNN;END=39348485;HGNCId=9969;REF=12;REPID=RFC1;RL=61;RU=AAAAG;RUMATCH;RankScore=1:10;STR_NORMAL_MAX=15;STR_PATHOLOGIC_MIN=300;STR_STATUS=normal,normal;SVTYPE=STR;VARID=RFC1;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/2:0/0:0/0:29/19:51:12-13/9-9:13/9:SPANNING/SPANNING:AR,AD::.:5981:1:U1:gt&gq&only_IP&vim&exit_u1
312
312
  chr4 41745972 . A <CNV:TR> . PASS CSQ=tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|PHOX2B|8929|Transcript|NM_003924.4|protein_coding|3/3||||835-894/2785|720-779/945|240-260/314||||1||-1||1|EntrezGene|||||||||||||||||||||||||||||||||||1|AD||||||||||||||||||||||LB|type&pick&gene_str&up_downstream&unit&status&exit_lb;Disease=CCHS;DisplayRU=NGC;END=41746032;HGNCId=9143;REF=20;REPID=PHOX2B;RL=61;RU=GCC;RUMATCH;RankScore=1:10;STR_NORMAL_MAX=20;STR_PATHOLOGIC_MIN=25;STR_STATUS=normal;SVTYPE=STR;VARID=PHOX2B;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/1:0/0:0/0:20.0/20.0:43:17-20/17-20:19/19:SPANNING/SPANNING:AR,AD::.:8929:1:U1:gt&gq&only_IP&vim&exit_u1
313
- chr5 146878728 . G <CNV:TR>,<CNV:TR> . PASS CSQ=tandem_duplication|feature_elongation&5_prime_UTR_variant|HIGH|PPP2R2B|5521|Transcript|NM_181675.4|protein_coding|1/10||||1-29/10828||||||1||-1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||LB|type&pick&gene_str&up_downstream&unit&status&exit_lb;Disease=SCA12;DisplayRU=CTG;END=146878757;HGNCId=9305;REF=10;REPID=PPP2R2B;RL=30;RU=GCT;RUMATCH;RankScore=1:10;STR_NORMAL_MAX=32;STR_PATHOLOGIC_MIN=43;STR_STATUS=normal,normal;SVTYPE=STR;VARID=PPP2R2B;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/2:0/0:0/0:18/17:35:14-16/10-11:15/11:SPANNING/SPANNING:AR,AD::.:5521:1:U1:gt&gq&only_IP&vim&exit_u1
313
+ chr5 146878728 . G <CNV:TR1>,<CNV:TR2> . PASS CSQ=tandem_duplication|feature_elongation&5_prime_UTR_variant|HIGH|PPP2R2B|5521|Transcript|NM_181675.4|protein_coding|1/10||||1-29/10828||||||1||-1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||LB|type&pick&gene_str&up_downstream&unit&status&exit_lb;Disease=SCA12;DisplayRU=CTG;END=146878757;HGNCId=9305;REF=10;REPID=PPP2R2B;RL=30;RU=GCT;RUMATCH;RankScore=1:10;STR_NORMAL_MAX=32;STR_PATHOLOGIC_MIN=43;STR_STATUS=normal,normal;SVTYPE=STR;VARID=PPP2R2B;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/2:0/0:0/0:18/17:35:14-16/10-11:15/11:SPANNING/SPANNING:AR,AD::.:5521:1:U1:gt&gq&only_IP&vim&exit_u1
314
314
  chr6 45422752 . C <CNV:TR> . PASS CSQ=tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|RUNX2|860|Transcript|NM_001024630.4|protein_coding|3/9||||416-464/5540|219-267/1566|73-89/521||||1||1||1|EntrezGene|||||||||||||||||||||||||||||||||||1|AD||||||||||||||||||||||LB|type&pick&gene_str&up_downstream&unit&status&exit_lb;Disease=CCD;DisplayRU=GCN;END=45422801;HGNCId=10472;REF=16;REPID=RUNX2;RL=50;RU=GCA;RUMATCH;RankScore=1:10;STR_NORMAL_MAX=17;STR_PATHOLOGIC_MIN=27;STR_STATUS=normal;SVTYPE=STR;VARID=RUNX2;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/1:0/0:0/0:18.0/18.0:39:14-15/14-15:15/15:SPANNING/SPANNING:AR,AD::.:860:1:U1:gt&gq&only_IP&vim&exit_u1
315
- chr7 27199679 . C <CNV:TR>,<CNV:TR> . PASS CSQ=tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|HOXA13|3209|Transcript|NM_000522.5|protein_coding|1/2||||360-412/5015|346-398/1167|116-133/388||||1||-1||1|EntrezGene|||||||||||||||||||||||||||||||||||1|AD||||||||||||||||||||||VUS|type&pick&gene_str&up_downstream&unit&status&exit_vus;END=27199732;REF=18;REPID=HOXA13_III;RL=54;RU=GCG;RUMATCH;SVTYPE=STR;VARID=HOXA13_III;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/2:0/0:0/0:48/2:51:16-17/13-13:17/13:SPANNING/SPANNING:AR,AD,AR_C:chr7_27199925_G_/:.:3209:1:U1:gt&gq&only_IP&vim&exit_u1
316
- chr7 27199925 . G <CNV:TR>,<CNV:TR> . PASS CSQ=tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|HOXA13|3209|Transcript|NM_000522.5|protein_coding|1/2||||126-166/5015|112-152/1167|38-51/388||||1||-1||1|EntrezGene|||||||||||||||||||||||||||||||||||1|AD||||||||||||||||||||||VUS|type&pick&gene_str&up_downstream&unit&status&exit_vus;END=27199966;REF=14;REPID=HOXA13_I;RL=42;RU=GCC;RUMATCH;SVTYPE=STR;VARID=HOXA13_I;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/2:0/0:0/0:43/7:52:13-15/7-12:14/11:SPANNING/SPANNING:AR,AD,AR_C:chr7_27199679_C_/:.:3209:1:U1:gt&gq&only_IP&vim&exit_u1
317
- chr8 104588961 . A <CNV:TR>,<CNV:TR> . PASS CSQ=tandem_duplication|feature_elongation&5_prime_UTR_variant|HIGH|LRP12|29967|Transcript|NM_013437.5|protein_coding|1/7||||260-297/4378||||||1||-1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||LB|type&pick&gene_str&up_downstream&unit&status&exit_lb;Disease=OPDM1;DisplayRU=CCG;END=104588999;HGNCId=31708;REF=13;REPID=LRP12;RL=39;RU=CGC;RUMATCH;RankScore=1:10;STR_NORMAL_MAX=45;STR_PATHOLOGIC_MIN=90;STR_STATUS=normal,normal;SVTYPE=STR;VARID=LRP12;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/2:0/0:0/0:13/19:35:15-16/12-12:16/12:SPANNING/SPANNING:AR,AD::.:29967:1:U1:gt&gq&only_IP&vim&exit_u1
318
- chr9 69037287 . G <CNV:TR>,<CNV:TR> . PASS CSQ=tandem_duplication|feature_elongation&intron_variant|HIGH|FXN|2395|Transcript|NM_000144.5|protein_coding||1/4|||||||||1||1||1|EntrezGene||||||||||||||||||||||||||||||||||||AR||||||||||||||||||||||LB|type&pick&gene_str&up_downstream&unit&status&exit_lb;Disease=FRDA;DisplayRU=GAA;END=69037304;HGNCId=3951;REF=6;REPID=FXN;RL=18;RU=AAG;RUMATCH;RankScore=1:10;STR_NORMAL_MAX=34;STR_PATHOLOGIC_MIN=66;STR_STATUS=normal,normal;SVTYPE=STR;VARID=FXN;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/2:0/0:0/0:2/23:31:17-17/9-10:17/10:SPANNING/SPANNING:AR,AD::.:2395:1:U1:gt&gq&only_IP&vim&exit_u1
315
+ chr7 27199679 . C <CNV:TR1>,<CNV:TR2> . PASS CSQ=tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|HOXA13|3209|Transcript|NM_000522.5|protein_coding|1/2||||360-412/5015|346-398/1167|116-133/388||||1||-1||1|EntrezGene|||||||||||||||||||||||||||||||||||1|AD||||||||||||||||||||||VUS|type&pick&gene_str&up_downstream&unit&status&exit_vus;END=27199732;REF=18;REPID=HOXA13_III;RL=54;RU=GCG;RUMATCH;SVTYPE=STR;VARID=HOXA13_III;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/2:0/0:0/0:48/2:51:16-17/13-13:17/13:SPANNING/SPANNING:AR,AD,AR_C:chr7_27199925_G_/:.:3209:1:U1:gt&gq&only_IP&vim&exit_u1
316
+ chr7 27199925 . G <CNV:TR1>,<CNV:TR2> . PASS CSQ=tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|HOXA13|3209|Transcript|NM_000522.5|protein_coding|1/2||||126-166/5015|112-152/1167|38-51/388||||1||-1||1|EntrezGene|||||||||||||||||||||||||||||||||||1|AD||||||||||||||||||||||VUS|type&pick&gene_str&up_downstream&unit&status&exit_vus;END=27199966;REF=14;REPID=HOXA13_I;RL=42;RU=GCC;RUMATCH;SVTYPE=STR;VARID=HOXA13_I;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/2:0/0:0/0:43/7:52:13-15/7-12:14/11:SPANNING/SPANNING:AR,AD,AR_C:chr7_27199679_C_/:.:3209:1:U1:gt&gq&only_IP&vim&exit_u1
317
+ chr8 104588961 . A <CNV:TR1>,<CNV:TR2> . PASS CSQ=tandem_duplication|feature_elongation&5_prime_UTR_variant|HIGH|LRP12|29967|Transcript|NM_013437.5|protein_coding|1/7||||260-297/4378||||||1||-1||1|EntrezGene||||||||||||||||||||||||||||||||||||AD||||||||||||||||||||||LB|type&pick&gene_str&up_downstream&unit&status&exit_lb;Disease=OPDM1;DisplayRU=CCG;END=104588999;HGNCId=31708;REF=13;REPID=LRP12;RL=39;RU=CGC;RUMATCH;RankScore=1:10;STR_NORMAL_MAX=45;STR_PATHOLOGIC_MIN=90;STR_STATUS=normal,normal;SVTYPE=STR;VARID=LRP12;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/2:0/0:0/0:13/19:35:15-16/12-12:16/12:SPANNING/SPANNING:AR,AD::.:29967:1:U1:gt&gq&only_IP&vim&exit_u1
318
+ chr9 69037287 . G <CNV:TR1>,<CNV:TR2> . PASS CSQ=tandem_duplication|feature_elongation&intron_variant|HIGH|FXN|2395|Transcript|NM_000144.5|protein_coding||1/4|||||||||1||1||1|EntrezGene||||||||||||||||||||||||||||||||||||AR||||||||||||||||||||||LB|type&pick&gene_str&up_downstream&unit&status&exit_lb;Disease=FRDA;DisplayRU=GAA;END=69037304;HGNCId=3951;REF=6;REPID=FXN;RL=18;RU=AAG;RUMATCH;RankScore=1:10;STR_NORMAL_MAX=34;STR_PATHOLOGIC_MIN=66;STR_STATUS=normal,normal;SVTYPE=STR;VARID=FXN;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/2:0/0:0/0:2/23:31:17-17/9-10:17/10:SPANNING/SPANNING:AR,AD::.:2395:1:U1:gt&gq&only_IP&vim&exit_u1
319
319
  chrX 25013650 . G <CNV:TR> . PASS CSQ=tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|ARX|170302|Transcript|NM_139058.3|protein_coding|2/5||||526-572/2893|298-344/1689|100-115/562||||1||-1||1|EntrezGene||||||||||||||||||||||||||||||||||||XL||||||||||||||||||||||VUS|type&pick&gene_str&up_downstream&unit&status&exit_vus;END=25013697;REF=16;REPID=ARX_I;RL=48;RU=GCC;RUMATCH;SVTYPE=STR;VARID=ARX_I;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/1:0/0:0/0:19.0/19.0:39:14-15/14-15:15/15:SPANNING/SPANNING:XLD,XLR::.:170302:1:U1:gt&gq&only_IP&vim&exit_u1
320
320
  chrX 137566828 . C <CNV:TR> . PASS CSQ=tandem_duplication|feature_elongation&coding_sequence_variant|HIGH|ZIC3|7547|Transcript|NM_003413.4|protein_coding|1/3||||703-730/4001|138-165/1404|46-55/467||||1||1||1|EntrezGene||||||||||||||||||||||||||||||||||||XL||||||||||||||||||||||LB|type&pick&gene_str&up_downstream&unit&status&exit_lb;Disease=VACTERLX;DisplayRU=GCN;END=137566856;HGNCId=12874;REF=9;REPID=ZIC3;RL=29;RU=CGC;RUMATCH;RankScore=1:10;STR_NORMAL_MAX=10;STR_PATHOLOGIC_MIN=11;STR_STATUS=normal;SVTYPE=STR;VARID=ZIC3;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/1:0/0:0/0:21.5/21.5:45:10-11/10-11:10/10:SPANNING/SPANNING:XLD,XLR::.:7547:1:U1:gt&gq&only_IP&vim&exit_u1
321
321
  chrX 147912051 . C <CNV:TR> . PASS CSQ=tandem_duplication|feature_elongation&5_prime_UTR_variant|HIGH|FMR1|2332|Transcript|NM_002024.6|protein_coding|1/17||||134-192/4441||||||1||1||1|EntrezGene||||||||||||||||||||||||||||||||||||XL||||||||||||||||||||||LB|type&pick&gene_str&up_downstream&unit&status&exit_lb;Disease=FX;DisplayRU=CGG;END=147912110;HGNCId=3775;REF=20;REPID=FMR1;RL=60;RU=GGC;RUMATCH;RankScore=1:10;STR_NORMAL_MAX=44;STR_PATHOLOGIC_MIN=200;STR_STATUS=normal;SVTYPE=STR;VARID=FMR1;VIPC_S=U1 GT:ADFL:ADIR:ADSP:LC:REPCI:REPCN:SO:VI:VIC:VID:VIG:VIM:VIPC_S:VIPP_S 1/1:0/0:0/0:20.0/20.0:44:29-31/29-31:30/30:SPANNING/SPANNING:XLD,XLR::.:2332:1:U1:gt&gq&only_IP&vim&exit_u1