Ensure ClinVar is filtering out significance terms

[AlistairNWard]

If the ClinVar significance contains a term Pathogenic,drug_response, does gene.iobio remove the non-significance terms (drug_response in this case) so that the displayed term is just Pathogenic? If not, the variant will not be flagged even though it is a pathogenic variant

[tonydisera]

In cases where more than one ClinVar significance is designated on a variant, gene.iobio will parse the multiple terms, and apply the filter criteria to the most pathogenic term. So, in your example, the variant will pass the filter ClinVar = 'pathogenic' because that term ranks higher than 'drug response'.

Another common scenario is a ClinVar variant with 'Benign/Likely Benign' dual designation. Here, 'Likely Benign' ranks higher, so it will be evaluated when the filter is applied. So this variant will pass a custom filter ClinVar = 'Likely Benign'. However, this variant will NOT pass the filter ClinVar = 'Benign'.

It could be argued that the filter logic should evaluate each term, passing the variant if ANY term matches. For example, as @AlistairNWard points out, 'drug response' is often coupled with another term. In these cases, the current logic will miss those variants with dual designations of 'drug response' + 'pathogenic' (or 'likely pathogenic').

[AlistairNWard]

We shouldn't be looking at any of the other terms (drug_response, risk allele etc) unless we explicitly want them in a different spot. These don't count as significance, the only terms that are a significance are:

Pathogenic Likely_pathogenic Uncertain significance Conflicting interpretations of pathogenicity Likely_benign Benign

I think Pathogenic/Likely_pathogenic is also an allowed term and doesn't need to be broken up