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.

[ahwagner]

I'm not sure I follow this change; if we are disallowing representation of variants outside of a specified reference (which I think is a good thing), when would we use +/- syntax? I am assuming this is still intended to be used since it is not being removed in this PR.

Is there an associated discussion / issue thread to provide context for what this PR is addressing?

[jfjlaros]

when would we use +/- syntax?

When we use a genomic reference sequence.

For example, description NG_012337.3(NM_003002.4):c.52+100del is valid because position c.52+100 indexes a G at position 5213 in the reference sequence of NG_012337.3.
On the other hand, description NM_003002.4:c.52+100del is invalid since c.52+100 does not index anything in the reference sequence of NM_003002.4.

[ahwagner]

In addition to the specific requested change, it was noted that this edited text continues to conflict with other parts of the website, which should now be updated to match this.

[ifokkema]

In addition to the specific requested change, it was noted that this edited text continues to conflict with other parts of the website, which should now be updated to match this.

Fixed in b167111. I will open a PR.