Community Consultation

NOTE

In the original proposal the descriptions included the nucleotide (A, C, G or T) that was identified as not changed (g.50377648A=, c.1823A=, n.611T=). It should be noted that, following existing HGVS standards (e.g. g.123456del, c.123dup) this addition is not necessary; g.50377648=, c.1823= and n.611= are correct and preferred HGVS descriptions.

Proposal SVD-WG001 (no change)

• Status: accepted

  proposal SVD-WG001 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 to allow description of variant tested but no change detected using the character “=” (equal to); g.50377648=, m.15366=, c.1823=, n.611=, r.377=, p.Val76=. The description should include the position(s) screened (nucleotides or amino acids) and the reference sequence used should always be mentioned.

Examples

DNA

• NC_000023.11:g.32867908=

  a screen was performed showing that nucleotide g.32867908 was a “G” like in the genomic reference sequence (the nucleotide was not changed).

• NM_004006.1:c.123=

  a screen was performed showing that nucleotide c.123 was a “C” like in the coding DNA reference sequence (the nucleotide was not changed).

  NOTE: the description c.123C>C is not allowed

• NM_004006.1:c.[123=;456=;789=]

  a screen was performed showing that nucleotides c.123, c.456 and c.789 (all on the same allele) were identical to the coding DNA reference (the nucleotide was not changed).

• LRG_199t1:c.[633A>G];[633=]

  a screen was performed showing that one allele carries variant c.633A>G and the other allele the reference sequence (a “A”).

  NOTE: LRG_199t1:c.[633A>G];[531_648=;961_1149=] specifies that only exons 7 (c.531 to c.648) and 10 (c.961 to c.1149) of the DMD gene were analysed.

• NM_001849.3:c.-1_*1=

  a screen was performed showing that nucleotides c.-1 to c.*1 of the COL6A2 gene (including the entire protein coding DNA sequence) were as in coding DNA reference sequence NM_001849.3 (exons only).

• NM_001849.3:c.=

  a screen was performed showing that the entire coding DNA reference sequence (NM_001849.3, exons only, incl. UTR’s) did not contain variants.

• LRG_476:g.4950_39800=

  a screen was performed showing that nucleotides g.4950 to g.39800 of the COL6A2 gene were as in the genomic reference sequence (LRG_476, exons and introns).

RNA

• NM_004006.1:r.470=   (c.470=)

  a screen was performed showing that nucleotide r.470 (on RNA level) was a “u” as in the RNA reference sequence (the nucleotide was not changed).

  NOTE: description of the variant at DNA level is mandatory

protein

• LRG_199p1:p.(Phe41=)   (LRG_199t1:c.123C>T)

  the predicted consequence of variant c.123C>T (DNA level) is that amino acid residue 41 is an “Arg” like in the protein reference sequence (the nucleotide was not changed, RNA was not analysed).

  NOTE: description of the variant at DNA level is mandatory (depending on the amino acid, up to 5 different DNA changes may leave the amino acid unchanged).

Original proposal