I want to recalculate the expected number of variants. I am very interested in the mutation rate table, can gnomAD provide it?
I know it’s been a while since the question was asked, but I it took me a bit to find this so maybe this will be useful to someone.
Supplementary Data 10 in this paper (The mutational constraint spectrum quantified from variation in 141,456 humans | Nature) provides a lookup table for mutation rates that is based on the reference, alternative, context, and methylation status of a variant
If you combine the information in this table with the methylation and context files described here:
you should be able to construct the mutation rate for all variants of interest. Hope this helps!