We are having a hard time to determine a "representative" amino acid change that resulted from a genomic point mutation. Obviously, a genomic point mutation in a coding region leads to a protein sequence change (including missense, nonsense, splice-variants... etc). Problem is, there are multiple possible transcripts (from a same gene) that are affected from the point mutation, and the result can be different for each transcript. For example, one mutation can be synonymous in transcript A, but missense in transcript B and nonsense in transcript C. Question is, if we need to pick one AA change, which transcript should we use?
I understand genomic mutation to AA change cannot be always 1 to 1. However in a usual biological paper, researchers tend to report only one AA acid change from one mutation. In my case, we are counting the ratio of missense, nonsense, synonymous... from a discovered mutation list, in which we need to assign one AA change type to one mutation.