I have a doubt regarding the ExAC database about the allele frequency. For some variants the allele frequency is over 50 %. How to interpret it. Does it mean that it is more frequent than the wild-type?
"Wild-type" isn't the correct term in (human) population genetics. I'd
say every one of us is equally wild regardless of presence or absence
of rare variants. The correct term and way of viewing this would be
"reference allele", meaning the allele which was found when
constructing the human reference genome (using a few donors - not one
sample). Therefore, it's very well possible (and indeed happens as you
see) that the reference allele isn't the major allele.