Tighten preset filter for moderate/high impact variants

[tonydisera]

Is the ‘Moderate or high impact’ preset filter in gene.iobio too permissive. Often, the majority of variants passing this filter are moderate impact variants that are hets and have a benign/likely benign ClinVar designation. This makes sense, given that these are variants that don’t pass the ‘Clinvar pathogenic’ or inheritance modes filters. Arguably, a moderate or high impact variant may play some role in the proband’s syndrome/disorder/disease. I just wonder if the criteria should be a bit more selective.

What are your thoughts on tightening this preset filter in the following way?

Show high impact (LOF) variants only. Lower the allele frequency to < 1% Exclude any variants with all benign/likely benign ClinVar designations unless there is a high REVEL score (or a predicted deleterious designation from SIFT or Polyphen)

[tonydisera]

Al - I think this is probably a good idea. We should really try and restrict the preset filters to highlight variants that have a real chance of being useful. If these turn up nothing, the user can relax filters on their own. Is it worth including a REVEL cutoff in the filter?

[tonydisera]

from Matt - I like this ideas. I think we'll just want to make sure we notify the user that these filters are applied and they can loosen them to bring more data in.

[tonydisera]

For now, I will just lower the allele frequency to <= 1 % and rename the filter to 'high'.

[mvelinder]

Done