Proposal SVD-WG002 (n. prefix)
- Status: accepted
- proposal SVD-WG002 was opened for Community Consultation on May 14 (2015), closing on Jul.16 (2015). Since no major objections were received the SVD-WG decided to accept the proposal on Oct.6 (2015). The proposal was part of the HGVS nomenclature version 15.11 update.
The proposal suggests to extend the HGVS recommendations by allowing the description of variants based on a non-coding DNA reference sequence indicated by the prefix “n”. In a non-coding DNA reference sequence nucleotide numbering starts with 1 at the first nucleotide of the sequence and ends at the last nucleotide. Intronic nucleotides are numbered as in a coding DNA reference sequence (see Numbering).
- an A to G change of nucleotide 345 in relation to a non-coding DNA reference sequence. Full description NR_028379.1:n.345A>G (FTX transcript, XIST regulator (non-protein coding) long non-coding RNA).
- the deletion of nucleotide 696-38544 in relation a non-coding DNA reference sequence; the variant is located in the 3’ half of the intron between nucleotides n.695 and n.696 (intron 5).
- NOTE: in this case, since a non-coding DNA reference sequence does not contain intron sequences, a genomic reference sequence has to be given, e.g. NC_000023.10(NR_028379.1):n.696-38544del.
The Committee noted concerns related to determining if a particular non-coding sequence is genuinely non-coding, in particular when such sequences do contain an open reading frame. It was felt however that the nomenclature system should match what the reference sequence record purports the sequence type to be. An alternative prefix “nc.” (Non-Coding) was suggested, but it was determined that the precedent of single-letter prefixes for reference sequence (g., c., r., p., m., etc.) should be conserved.