How should I refer to one type of dbSNP in publications

Question

[timing]

Assuming I would like to discuss something interesting about the gene when an adenine was substituted by a guanine (A>G as recorded in rs268), what is the appropriate nomenclature for me to do so? Is it appropriate to say rs268 variant when referring to the substituted sequence and rs268 wildtype when referring to the consensus sequence? What should I say if there are more than one substitutions recorded in the dbSNP entry?

Any input will be appreciated. Thanks in advance!

Answer 1

[Emily]

The correct terminology is "reference" and "alternative" (or "ref" and "alt"). The reference is whatever is in the reference genome, and is always listed first in allele strings. It is not necessarily the major, ancestral or wildtype allele, but it is in the reference genome so it is the reference allele. The alternative is whatever is not in the reference genome.

[timing]

Thank you very much! In the case of multiple substitutions e.g. A is substituted by both G and T, may I know which terminology can I use to specifically refer to either G or T?

[Emily]

Be explicit. Say G or T.

[timing]

Thanks! May I kindly check nomenclature like rs268 (G) is acceptable when referring to the substitution by G?

[Emily]

There's no fixed nomenclature. That would be completely clear.