There are existing frameworks for integrating functional and statistical fine mapping methods (e.g. polyfun + susie/finemap). They use annotation overlaps like

There are existing frameworks for integrating functional and statistical fine mapping methods (e.g. polyfun + susie/finemap). They use annotation overlaps like epigenetic or conservation tracks but can be extended to variant effect predictions from models like this. They essentially modify the prior probability of a variant being causal from uniform to one that depends on the functional annotation.