REF and ALT alleles seem to be wrong way round in dbSNP
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2.8 years ago
Charlie2 ▴ 50

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 • 677 views
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2.8 years ago

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

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Thank you, that's really helpful.

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

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Perfect.

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