coding/non-coding identity

[jtdendunnen]

as discussed in HVNC meeting, there should be no difference in the description of this rule for coding and non-coding reference sequences

[ifokkema]

@jfjlaros I believe this was the sentence that you mentioned, correct?

[jfjlaros]

Indeed.

Additionally, instead of using "reference sequence", I would propose to use something like "transcript annotation", e.g., "it is not allowed to describe variants in nucleotides beyond the boundaries of the annotated transcript."

[ifokkema]

Additionally, instead of using "reference sequence", I would propose to use something like "transcript annotation", e.g., "it is not allowed to describe variants in nucleotides beyond the boundaries of the annotated transcript."

I believe, however, that this remark is meant to exclude NR_123456.1:n.100+10del. If so, the current statement is fine. Although it seems not to be allowed to describe NC_000001.10(NR_123456.1):n.-100del either, I do not believe that is what is meant here. Perhaps we should update the sentence and clarify what is meant here; intronic positions (that then require the addition of a genomic reference sequence) or anything beyond the transcript boundaries (even when used in combination with a genomic reference sequence). If both are meant, this should be clarified.

[jfjlaros]

Indeed, it should never be allowed to address a coordinate outside of the reference sequence, regardless of the coordinate system used. Perhaps we should make this a general remark.

If this was indeed the intention, then addressing genomic coordinates beyond the boundaries of the transcript was never a rule in the first place. If this is the case, then I would prefer a general remark and dropping the comments in the "coding" and "noncoding" sections.