Accepted - SVD-WG002

Proposal

The proposal SVD-WG002 (n. reference sequence) suggested to extend the current HGVS recommendations to allow the use of a non-coding DNA reference sequence. The Community Consultation closed on July 16 (2015). All comments were collected and discussed by the SVD-WG on Oct.6. Since no major objections were received the proposal was accepted. The proposal will be part of the HGVS recommendations version 2.1511.

Non-coding reference sequence prefix: n.

When a non-coding DNA reference sequence is used for nucleotide numbering the prefix "n." should be used. Nucleotide numbering in the non-coding DNA reference sequence 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.

Examples;

• n.345A>G  describes an A to G change of nucleotide 345 in relation to a non-coding DNA reference sequence
        Full description NR_028379.1(FTX):n.345A>G  (FTX transcript, XIST regulator (non-protein coding) long non-coding RNA)
• n.696-38544del  describes 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: since a non-coding DNA reference sequence does not contain intron sequences a genomic reference sequence has to be given as well.  Full description NR_028379.1(FTX):n.696-38544del, genomic reference sequence NC_000023.10.

NOTE:  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.

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