Incorrect gene_id in request https://civicdb.org/api/variants

[SerDImIgor]

The number of unique values in https://civicdb.org/api/genes is 328, and the number of unique genes referenced by variants is 467. From this we can conclude that some variants refer to genes that do not exist.

[acoffman]

Hi @SerDImIgor, thanks for your interest in CiVIC. What you're seeing here is a result of the scoping we do by default on the API endpoints.

The /api/genes endpoint returns only genes that have at least one evidence item in the accepted state, however the /api/variants endpoint will return all variants that have at least one evidence item in any state attached to them. As such, you will find variants that reference genes that are not returned in the /api/genes endpoint; these will be variants that have evidence attached to them, but that evidence is still pending review. I agree this is a little confusing. We will discuss standardizing on one scope or the other and I'll get back to you with the answer.

Thanks, Adam