Variant effect prediction REF mismatch

[okurman]

Dear Selene/Sei developers, thank you for the colossal work you've undertaken.

I have a question regarding the variant effect prediction functionality of Sei model. I am using the model to calculate the variant effects using gnomAD, there seem to be many mismatches between the REFs of the gnomAD variants and the GRCh38 assembly fasta file. So, my question is, in these cases, does Selene use the REF of the given VCF file or does it use the corresponding NT from the GRCh38 fasta file?