Using Annovar, one of my non-synonymous variant has an alternate allele which is present in about 99% of the population (according to 1000Genomes database), but is also described as pathogenic according to CLINVAR, dbSNP and other association study databases.
dbSNP link here. It is a single nucleotide substitution from G (ref) to C (alt).
According to dbSNP, Global MAF from 1000 Genomes: G=0.0018/9 C=0.997/4994
Does it make sense? Would it mean that ~100% of the population would be "sick" in this case?