For a case-control study, the minor allele frequency is the ratio of chromosomes in the population carrying the less common variant to those with the more common variant. I want to know if it is still the mutant one.
The "Major and "Minor" alleles at any given SNP in any given population, are just that and no more - the major is present with higher frequency than the minor.
I personally never refer to the minor allele as a "mutant", preferring the term "variant". The reason for this is that "mutant" implies some functional causality ".. this is mutated in colon cancer". Not all alleles have a known functional role. Besides, "mutant" and "variant" are not the same.
So - since people use the term "mutant" very loosely - particularly if their first language isnt English - this can cause confusion as you have already experienced. I'd stick with your use: "variant"
The "Major and "Minor" alleles at any given SNP in any given population, are just that and no more - the major is present with higher frequency than the minor.
I personally never refer to the minor allele as a "mutant", preferring the term "variant". The reason for this is that "mutant" implies some functional causality ".. this is mutated in colon cancer". Not all alleles have a known functional role. Besides, "mutant" and "variant" are not the same.
So - since people use the term "mutant" very loosely - particularly if their first language isnt English - this can cause confusion as you have already experienced. I'd stick with your use: "variant"