REF and ALT alleles seem to be wrong way round in dbSNP

Question

[Charlie2]

This is probably a really stupid newbie question, but I'm looking at rs1529927 in dbSNP and confused to see that although it gives the Alleles as:

Alleles C>G

it then gives Frequency as:

Frequency C=0.02066 (2594/125568, TOPMED) C=0.02443 (2966/121398, ExAC) C=0.0230 (710/30822, GnomAD) (+ 5 more)

If C is the major allele and G the minor, how come C is listed as so rare?

Answer 1

[i.sudbery]

C is not the major allele, its the reference allele. The reference allele is the base at that position in the individual that provided that part of the original human genome sequence, there is no guarantee that it is the most frequent allele.

[Charlie2]

Ah, thank you - I'm very new to all this and get confused with the terminology.

[Kevin Blighe]

See also: A: Alternate nucleotide is more frequent than reference nucleotide. OMG I'm dizzy.

[Charlie2]

Thank you, that's really helpful.

[GenoMax]

If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one if they work.

[Charlie2]

Ah, thanks, still learning how it all works. I think I've marked it as solved now.

[GenoMax]

Perfect.

[Ram]

Please do not delete the post after it's been answered.