ClinVar benign/pathogenic counts too broad
The code
self.session.query(
clinvar_clinsigs.c.allele_id,
count_matches("%pathogenic%").label("pathogenic"),
count_matches("%uncertain%").label("uncertain"),
count_matches("%benign%").label("benign"),
)
includes clinical significance descriptions like no known pathogenicity
in pathogenic
(and not in benign
) category. See if we can find an exhaustive list of clinical significance descriptions for this.