296
edits
Changes
→Chosing the correct variants to include in the PGx alleles
| NC_000010.10(GRCh37) || Source API: g.96522561T(rs17885098), g.96602623G(rs3758581), g.96522613A>G, g.96609568T>C(rs4917623)|| Source VCF: g.96521422A>G(rs7902257), g.96522613A>G || Source GitHub: g.96522613A>G(by liftOver) || Disagree on rs4917623(intron), rs7902257(2kb upstream variant). rs17885098 and rs3758581 are included here because PharmGKB assume different reference bases for these positions (seems like a problem caused by change of Major allele between reference builds GRCh37/GRCh38. Note that refSeq also agrees with GRCh38 and not GRCh37)
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| NC_000010.11(GRCh38) || Source Pharmgkb.org: g.94762856A>G || Source VCF: g.94762804C>T(rs17885098), g.94762856A>G, g.94842866A>G(rs3758581) || Source GitHub: g.94762856A>G || PharmGKB does not agree with itself when reporting GRCh38 variants on the homepage and GRCh37 variants in the API. The differences probably caused by non-standard use of Major/Minor Allele (rs17885098, rs3758581) with respect to dbSNP, and removing intron variants (rs4917623) in the Excel sheet may be sensible from an exon/protein-coding view.
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