296
edits
Changes
→Chosing the correct variants to include in the PGx alleles
! CYP2C19*19 !! PharmGKB !! PharmVar !! PharmCAT !! Comment
|-
| NC_000010.10(GRCh37) || g.96522561T(rs17885098), g.96602623G(rs3758581), g.96522613A>G, g.96609568T>C(rs4917623)|| g.96521422A>G(rs7902257), g.96522613A>G || g.96522613A>G(by liftOver) || Disagree on rs4917623(intron), rs7902257(2kb upstream variant). Disagree on requirement that rs17885098 and rs3758581 must be reference (i.e. only PharmGKB require that these coordinates are not missing). The reason that included here because PharmGKB has included these positions is that they assume different reference bases for these positions (seems like a problem caused by change of Major allele between reference builds GRCh37/GRCh38, which is inverted in PharmGKB vs dbSNP . Note that refSeq also agrees with GRCh38 and LiftOvernot GRCh37)
|-
| NC_000010.11(GRCh38) || g.94762856A>G || g.94762804C>T(rs17885098), g.94762856A>G, g.94842866A>G(rs3758581) || g.94762856A>G || PharmGKB does not agree with itself when reporting GRCh38 variants in Excel sheets and GRCh37 variants in the API. The differences probably caused by non-standard use of Major/Minor Allele (rs17885098, rs3758581) with respect to dbSNP. Filtering out intron variants (rs4917623) in the Excel sheet may be sensible from an exon/protein-coding view.
