multiple effect and reference allele definitions in PGS001405

[pgscatalog]

multiple effect and reference allele definitions in PGS001405

[smlmbrt]

Dear @kaurao, thanks for your message.

The variants in the first set of examples are insertions/deletions noted in the VCF formatting: using the nucleotide before the variants and using the position of this nucleotide (n-1).

In the second set of examples, these are variants where the rsID wasn't provided, but the chromosomal position was which is sufficient for variant matching with the genome build information (GRCh37). CHR/POS can be more advantageous than just the rsIDs as the identifiers sometimes change between releases of dbSNP whereas the positions and reference nucleotides do not.

As a general note all the variant information in the scoring files is identical to how the authors have provided it, so differences in notation across scoring files are to be somewhat expected. Hope that answers the question, let us know if we can help more!