It seems that all the well-known annotation tools implicitly assume that the reference allele (identical to the allele of the human reference genome) is the normal one and the functional annotation is on whether alternative allele may cause any damage to the corresponding gene/transcript. Is not it possible that some of the alleles appearing on the reference genome are actually the deleterious ones?
Md. Mostafijur Rahman
It's true that the reference allele is sometimes deleterious for a specific population. But it varies from population to population. Study on different population give different type of result for a specific SNP. You can try 1000 genome database or regulomedb to find deleterious effect of a genotype.
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