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.