Not all variants are annotated with AF - expected or a problem?

Question

[Luiz]

I tried to use built-in databases and build my own (snpEff), however, in both cases, not all my variants are annotated with Allele Frequency (AF). The problem is: those variants not annotated in VCF has Alelle Frequency in dbSNP (ncbi website). I tried dbSNP and dbNSFP.

I would like to discuss if such behavior is expected. I am using the latest version available for every software or database (dbSNP, snpEff, dbNSFP), GRCh38.p14 / GRCh38.105. It's worth mention that i observed the same phenomenon in Variant Effect Predictor. I am using HaplotypeCaller as my variant call software.

[Pierre Lindenbaum]

I would like to discuss if such behavior is expected

yes if your variant is rare , it's unknown in the databases.

[crisime]

Can you post an example of an entry where your vcf does not have an AF annotation but you would expect one because it is in dbsnp and your snpeff call.

[crisime]

And check whether your variant exists and has an AF in your downloaded data, not just on the NCBI-website. Maybe there is a data-discrepancy.