Actual Reference For This Dbsnp Entry?

Question

[nmb]

According to the dbSNP entry for rs2476601, the variant is at position 114377568 of chromosome 1, which is an A in both hg19 and GRCh37.p13. But some of the HGVS names for the SNP are "NG_011432.1:g.41808C>T" and "NM_012411.4:c.1693C>T". Why is the reference a C in these transcripts, if they refer to the same variant?

Secondary question: why is "NP_036543.4:p.Arg565=" listed, but "NP_036543.4:p.Arg565Trp" not?

Thanks for looking!

Answer 1

[GANI]

Although the base A is present in the reference genome (hg19) at this location (114377568), A is the minor allele for this position. Check the following link - illustrating the variation of this position (in GRCh37) from the 1000 genomes data. The major allele is G, and hence you see C as the reference in most transcripts.

http://www.ncbi.nlm.nih.gov/variation/tools/1000genomes/?cfg=NCID_1_1577973_130.14.18.128_9146_1388161264_32532969

For the second question, I think this is an issue (or intended truncation) with the NCBI website. In the summary view , you can view the full list of HGVS names for a given variation (see link below). However, some HGVS names are truncated in the detailed view.

http://www.ncbi.nlm.nih.gov/snp?Db=snp&Cmd=DetailsSearch&Term=2476601[uid]!