Partial intron retention #27
Description
Hello,
Partial intron retention at the RNA level returns the error "Positions not consecutive" when HGVS nomenclature is used.
For example using HGVS splicing examples from https://varnomen.hgvs.org/recommendations/RNA/variant/splicing/ like NC_000023.11(NM_004006.2):r.649_650ins650-50_650-1 gives the error "Range positions 649_650 not consecutive in insertion location".
Same issue for a variant I am studying that leads to partial retention of the last 12 bases of an intron NC_000008.11(NM_017780.4):r.3522_3523ins3523-12_3523-1. "Range positions 3522_3523 not consecutive in insertion location"
If I code it at the c. level with the sequence of the insertion of 12 bases NM_017780.4:c.3522_3523insgtccttttttag, then it returns it as NC_000008.11(NM_017780.4):c.3523-10_3524dup. Basically due to 3' rule it shifts the variant as a duplication of the 10 last base of the intron plus the 2 first bases of the last exon after the 2 first bases of the last exon since the 2 first bases of the insertion are the same than the 2 first bases of the exon. It is correct based on c. coding but as I specifically analyzed RNA, it is a true partial intron retention and I cannot get the real nomenclature of the mutation.