Allele with high population frequency also tagged as pathogenic

Question

[user31888]

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?

[Devon Ryan]

Post the variant and the rsID...

[Tonor]

Just to check, is it the non-synoymous variant that is called as "pathogenic" or the alternate allele? And the alternate allele is the one found in 99% of the population.

[WouterDeCoster]

Please be as informative as possible when asking a question.