Comments (1)
jfjlaros
commented on July 28, 2024
This is expected behaviour.
As you correctly point out, the two reference sequences differ, therefore HGVS descriptions of variants that lie on these reference sequences can also differ.
It is very unfortunate that the accession number of a transcript can be used in multiple ways. This is likely the source of much confusion. In your first example (NC_000002.11(NM_015120.4)) the string NM_015120.4 is used as a selector, it selects the transcript that is labeled NM_015120.4 in the annotation of NC_000002.11. In your second example the string NM_015120.4 is used as a proper accession number.
I hope this clarifies it a bit.
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