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KnownVar

KnownVar is an annotation layer that allows users to check whether that "precise" variant has been reported in literature. It leverages multiple variant databases (inc: ClinVar, OMIM, HGMD). This is anticipated to be most useful for Sequencing Clinic and similar studies of rare mutations.

Additional features include:

  1. Indicator function whether the gene has a disease-associated with it in OMIM
  2. Information of all disease names linked to gene in OMIM
  3. Report sites where a mutation has been linked to disease (but not the exact variant observed in patient of interest).
  4. Permitting screening of disease-associated mutations 2bp either side of variant of interest.
  5. Providing OMIM allelic variant (where available).
  6. Providing ClinVar "pathogenic/other" details (where available).
  7. Providing a HGMD assessment of pathogenicity of the variant (where available).

A complete update off all resources will occur bi-annually (June and December). ClinVar and OMIM will be updated on a more regular quarterly schedule (including March and September).

See how to run the function here:
List Known Var

This annotation layer will continue to grow with bioinformatics signatures. Contact Slavé for more information about upcoming bioinformatics signatures.