Open for comments - SVD-WG002


Published:  May 14, 2015
Closes:  July 16, 2015


Proposal


SVD-WG002 suggests to extend the current HGVS recommendations for the description of sequence variants with the proposal below. Comments can be sent to the HGVS/HVP/HUGO Sequence Variant Description Working Group (SVD-WG), addressed to "Varnomen @ variome.org", Subject: SVD-WG002. Comments need to be sent ultimately July 16, 2015.

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.

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.

Examples;


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