Question: REF and ALT alleles seem to be wrong way round in dbSNP
0
gravatar for Charlie2
3 months ago by
Charlie230
Charlie230 wrote:

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 • 207 views
ADD COMMENTlink modified 3 months ago • written 3 months ago by Charlie230
5
gravatar for i.sudbery
3 months ago by
i.sudbery4.3k
Sheffield, UK
i.sudbery4.3k wrote:

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.

ADD COMMENTlink written 3 months ago by i.sudbery4.3k

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

ADD REPLYlink written 3 months ago by Charlie230
1

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

ADD REPLYlink written 3 months ago by Kevin Blighe41k

Thank you, that's really helpful.

ADD REPLYlink written 3 months ago by Charlie230
1

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

ADD REPLYlink written 3 months ago by genomax65k

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

ADD REPLYlink written 3 months ago by Charlie230
1

Perfect.

ADD REPLYlink written 3 months ago by genomax65k

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

ADD REPLYlink written 3 months ago by RamRS21k
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