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ClinGen / clincoded

This GCI/VCI 1.0 platform has now been retired, and replaced with our new 2.0 platform:
https://github.com/ClinGen/gene-and-variant-curation-tools/issues
MIT License
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Investigate gnomAD data and variantType #2267

Closed cgpreston closed 2 years ago

cgpreston commented 3 years ago

Some users have reported not being able to see gnomAD data for variants in the VCI, examples:

  1. CA16020812
    • Note: this variant is also showing the warning "The current variant is in a non-coding region." in the "ClinVar Variants" section, which is incorrect.
  2. CA8814993
  3. CA501078
  4. CA190727690
  5. CA586896135

This issue was reported after the 2.0 release and investigated by @markmandell in CLINAWS-452 for variant CA8814993. Mark reported that the issue was related to the variantType value not being correct.

To investigate:

  1. Is an incorrect/missing variant type common among variants that only have CAR IDs?
  2. Or is there another reason these variants have the wrong variantType value?
  3. Can we fix the "variantType" issue to show gnomAD data?
  4. If we can't fix the variantType issue: Can we show gnomAD data for all variants somehow else?
    • There is a concern that our gnomAD data relies on a data transposition that may be wrong for some variant types, so the project would be to ensure that removing variantType from that logic wouldn't create other/more issues.
cgpreston commented 2 years ago

Replaced by https://github.com/ClinGen/gene-and-variant-curation-tools/issues/81