Hi, I've accidently noticed that an SNP with close to 1 allele frequency in Gnomad exom does not show up in gnomad Genome and that is something that turns out to have a consequence for the automatic ACMG annotation.
The SNP is https://www.ncbi.nlm.nih.gov/snp/rs142200057 It has almost zero frequency of reference allele in any database, but OK, I can leave with it...BUT: Thing is, that the reference was never found in gnomadV3. And when I'm performing annotation with some annotator using gnomadV3 (and not V2) it tells me that current snp is not found in Gnomad.v3 therefore it seems to be extremely rare and therefore might be pathogenic (which is absolutely not the case)
I went to the gnomad site downloaded chr2 gnomad v3 (https://storage.googleapis.com/gnomad-public/release/3.0/vcf/genomes/gnomad.genomes.r3.0.sites.chr2.vcf.bgz) and indeed there is neither rs142200057 in the file nor GGGG indel in given position
I then went and downloaded gnomad v2 exomes (https://storage.googleapis.com/gnomad-public/release/2.1.1/vcf/exomes/gnomad.exomes.r2.1.1.sites.2.vcf.bgz) and finally found there rs142200057 with alternative allele frequency of AF=9.99979e-01
My question is - why rs142200057 did not shows up in GnomadV3? It seems that due to the fact that Ref was never seen in that position it was filtered out due to some pipeline bug? However, when Ref has at least some frequency (Gnomad V2 exoms) everything is correctly represented.