10 weeks ago by
Santiago de Compostela, Spain
Quick answer: you're dealing with different references, therefore the reference alleles can differ, therefore the frequencies can differ too.
If you check rs73976541 on gnomAD v2.1.1 you're using GRCh37, where the change of the reference C for an alternative T occurs at a global frequency of ~0.005 and ~0.02 respectively in the exomes and genomes analyzed.
If you check rs73976541 on gnomAD v3.1 you're using GRCh38, where the change of the reference T for an alternative C occurs at a global frequency of ~0.9795 in the genomes analyzed.
So changing from GRCh37 to GRCh38 changed the reference allele for rs73976541! Unexpected for the untrained eye, but it can happen as you can see yourself on dbSNP. The take home message would be that the frequency refers to a particular allele, and not to the variant as a whole.