Hi - when using VEP to get allele frequency information for a list of SNPs, I ask for the gnomad_AF column. I have noticed however that around a third of my list return an NA value. How should I intepret this? Is that of all combined frequency consoritums across multiple continents, this SNP has never been seen (i.e. Ultra Rare)? Some of the SNPs do appear in dbsnp however, but I guess the exomes/genomes used for gnomad might not coincide with those reported to dbSNP? This seems about right to me - any lab can report to dbSNP, but only subset of the population end up in consotriums such as 100k genomes and exac.

Could anyone provide a definitive answer on this? Can I count them as "ultra rare" if a SNP does not appear in gnomad?

Thanks
I think it does count as ultra rare if gnomAD doesn't have it. As long as the comparing tool is configured well in comparing multi-allelic sites (as in, you're *sure* the variant is not in gnomAD), it can be labelled ultra-rare.