Show clinical variants on gene models

[eweitz]

This adds clinical variants to gene model diagrams. It enables users to see small variations and how they relate to disease.

Because Gene Leads shows protein domains in the same coordinate space, these place variations are especially useful.

Here's how it looks!

Show_clinical_variants_on_gene_models__Ideogram_2025-02-18.mov

Variants are shown as triangular "lollipops" atop the gene model. Hovering over a variant shows its basic genomic position and allele data, clinical significance, and a related disease. If available, a dbSNP ID (a.k.a. RS ID) is shown by default, as are less-common attributes like high review status (3+ stars). Clicking on a variant shows more detailed information, e.g. all related diseases, variant type, review status, origin, allele frequency, and ClinVar Variation ID.

Data comes from ClinVar. Only small variants with high signal are shown. Here "high signal" means the variant has a clinical significance of "pathogenic", "pathogenic / likely pathogeni" or "likely pathogenic", and a clinical review status of 2 stars or above (i.e. "criteria provided, multiple submitters, no conflicts", "reviewed by expert panel", or "practice guideline"). The associated pipeline #378.