dbNSFP lacks data for reference allele?
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8 months ago
Maia • 0

If I am understanding correctly, dbSNFP (3.5c) does an extremely extensive annotation for all variants from the reference genome. For example, if a position (hg38) is a G in there reference, the entry in dbNSFP covers all the variations of that:

1, 21864961, G > A 1: 21864961, G > C 1: 21864961, G > T

with various columns of annotation that describe each variant. In the example here, the 1000Gp3_AF allele frequency of G>A is 0.69 (other AF are null). If I interpret that to mean that A is the major allele at that position, and G is a minor allele, then there is no entry in dbNSFP for the minor allele, G, at that position.

In my case, I am interested in having information about the annotations and scores (such as conservation) about specific alleles. Is my understanding correct and that this data isn't in dbNSFP?

Thank you for the help, Maia

annotation dbNSFP SNP • 189 views