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

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?

snp dbsnp
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written by Charlie2 • Charlie2

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

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written by Charlie2 • Charlie2

You should really search the site before you create a new post. Also, this reply is better suited as a comment on i.sudbery's answer. Could you make the appropriate change please? That would involve the following steps:

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Thank you!

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written by Ram Ram

1 answer

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.

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written by i.sudbery i.sudbery

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

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written by Charlie2 • Charlie2

Thank you, that's really helpful.

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written by Charlie2 • Charlie2

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.
Upvote|Bookmark|Accept

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written by GenoMax GenoMax

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

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written by Charlie2 • Charlie2

Perfect.

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written by GenoMax GenoMax

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

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written by Ram Ram

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