sambaxter
commented
1 year ago We should also add a flag for when there are homozygotes in gnomAD. Ideally when you hover over the flag it tell you how many homozygotes.
Edit (rhgrant): added task to main description so that Github picks it up as a sub task
Right now we have a flag for "genomes only" and "filtered" but a few other flags would also be useful to add. If flags have multiple flags we may have to figure out how to display multiple flags.
[x] 1). In addition to "genomes only" we should add a flag for whenever the AN is less than 50% of than the highest AN. I think gnomAD as a similar warning so we may be able to pull that logic (an example variant). The label for the flag should be "Low AN" and the explanation in the hover over can copy the gnomAD warning "This variant is covered in fewer than 50% of individuals in gnomAD v2.1.1 exomes. Allele frequency estimates may not be reliable."
PR: #219
[x] 2). I would like to add a flag to any variant that has a higher AF than the most common ClinVar Pathogenic or Likely Pathogenic variant. For example if you look at this list and sort by frequency 13-52520435-C-T, 13-52534410-C-T, and 13-52520508-G-A should all have this flag since they have a higher AF than 13-52518281-G-T. The name of this flag should be "High AF" and the explanation should be "This variant has a higher allele frequency than the most common ClinVar pathogenic/likely pathogenic variant. It is important to establish whether this variant is disease-causing. Please use caution when including this variant in genetic prevalence estimates." This flag should not show up for any ClinVar path or likely path variants.
PR: #171
[x] 3). We should also add a flag for when there are homozygotes in gnomAD. Ideally when you hover over the flag it tell you how many homozygotes
PR: #237
Edit: (rhgrant) editing this list directly (addding linked PRs, checking boxes) as I work through these.