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populationgenomics / automated-interpretation-pipeline

Rare Disease variant prioritisation MVP
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ClinVar hyperlinks busted #389

Closed MattWellie closed 1 week ago

MattWellie commented 1 week ago

Old report example:

ANO5 variant, hyperlink http://www.ncbi.nlm.nih.gov/clinvar?term=269979[alleleid] loads the page https://www.ncbi.nlm.nih.gov/clinvar/variation/269979/?oq=269979[alleleid]&m=NM_213599.3(ANO5):c.1213C%3ET%20(p.Gln405Ter) (correct)

New report example: RNU4-2 variant, hyperlink http://www.ncbi.nlm.nih.gov/clinvar?term=3068742[alleleid] loads the page https://www.ncbi.nlm.nih.gov/clinvar/variation/2903249/?oq=3068742[alleleid]&m=NM_003442.6(ZNF143):c.272T%3EC%20(p.Val91Ala) (incorrect, a ZNF143 variant)

The general structure of the URL/query is unchanged, but the ID number I'm using has swapped from the AlleleID to the VariationID in the latest ClinVar changes. As evidence, https://www.ncbi.nlm.nih.gov/clinvar/variation/3068742/ loads the intended RNU4-2 variant, but https://www.ncbi.nlm.nih.gov/clinvar/variation/269979 gives a "Variation ID 269979 does not exist" message, which is correct.

MattWellie commented 1 week ago

https://github.com/populationgenomics/automated-interpretation-pipeline/blob/d57e4caf707e181e6279198e8b6f90ec3a32580c/reanalysis/summarise_clinvar_entries.py#L557

contrasted with the previous (correct)

https://github.com/populationgenomics/automated-interpretation-pipeline/blob/5dcdff96bfa521847b40c139887e25340b847014/reanalysis/summarise_clinvar_entries.py#L532