Why some SNP's allele frequencies in gnomAD are so different between v2 and v4?

Question

[liaotsungjen]

In gnomAD v4, for example, the allele frequency of rs1047989 in non-Finish European is 0.1451, and this SNP's AF in 1KG is 0.1086. However, in v2, rs1047989's AF in non-Finish European is 0.5004. I also checked this SNP in dbSNP, and it shows this SNP's AF in European of 1KG is 0.5358. Why is there a huge different in AF in gnomAD between GRCh37 and GRCh38? Also, are AF data in dbSNP based on GRCh37?

Answer 1

[Jeremy Leipzig]

That SNP is in an HLA gene which has had a lot of attention and improvement over the years, ranging from kits to software to the reference genome. I agree it would be interesting to see what really caused the change but I suspect the v2 AF is less accurate than v4.