CNV Gene Nomenclature - Helsinki Workshop
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Joint meeting of HGNC and HGVS: Room 209, Helsinki Fair Centre, Finland 31 May 2006( ~80 people in attendance)
Following a vote VCN genes will now be referred to as copy number variant or CNV genes (10 votes for CNV, 2 votes for VCN)
As a result of this meeting the HGNC formulated the following summary which will shortly be refined and incorporated into our Guidelines:
- HGNC is not a variation database.
- HGNC agrees with the need to 'name' individual copies of CNV genes.
- HGNC will continue to provide a unique "gene symbol" for all unique "genes".
- A unique "CNV symbol" will be available for "CNV genes".
- "CNV symbol" will be a new category in the HGNC database, with a unique symbol identifier which can be placed on a reference genome and the CNV symbol entry will include links to other databases.
- When a gene is identified as CNV then there will be a link in the gene symbol entry to any associated CNV symbol entries and to the Database of Genomic Variants.
- The CNV symbol entries will link to their stem symbol entry.
- "CNV symbols" will use the appropriate unique "gene symbol" stem with the addition of either a numeral or a letter depending on the last character in the stem symbol. eg: for the gene symbol "DEFB104" there will be 2 CNV symbols "DEFB104A" and "DEFB104B", whereas the gene symbol "ABO" could be given CNV symbols "ABO1", "ABO2" etc.
- "CNV symbols" will not have the same status in the HGNC database as "gene symbols".
- Standard gene search will only retrieve "gene symbols", eg DEFB104.
- The advanced search option to include CNV entries would retrieve DEFB104, DEFB104A, DEFB104B
- The use of CNV status means that there is no need for the addition of any extra identifiers in the gene name.
- HGNC will provide a "CNV symbol" upon request when the following criteria are reached:
- The "CNV gene" is listed in the Database of Genomic Variants
- NCBI and VEGA (if annotated by VEGA) agree upon the co-ordinates for the CNV copy in a reference sequence
- The "CNV genes" are greater than 97% identical