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.
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.