Wrong Accession submitted in ClinVar tests

[northwestwitch]

Got this email this morning. It's something we should fix before the next release!

Hi Chiara,

Our developers reported this morning another three API test submissions that
failed because the variant description includes rs150008607 in the Accession
field. Please address this issue before continuing to submit tests. Do you
have any questions?

[northwestwitch]

By looking at the schema, Accession is one of the keys of chromosomeCoordinates:

Perhaps they want a ClinVar accession ID instead of a dbSnp ID in that field?

I think I'll move this issue to preClinVar, as the wrong parsing of the text file is done there: https://github.com/Clinical-Genomics/preClinVar/blob/ecb7741625b92a8f7e5d7f618824a5712ce6fce9/preClinVar/file_parser.py#L200

[dnil]

Great! And it would not show in the csv and interfere with manual submission? I didn't see any for a couple of vars I tried, but I didn't quite take the time to hunt it down. 😊

[northwestwitch]

It will show, but shouldn't be a problem The fields of the CSV files haven't changed. That key/value corresponds to the variation IDs: https://www.ncbi.nlm.nih.gov/clinvar/docs/spreadsheet/#variation_ids