SVD WG001

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 nomenclature (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 July 16, 2015. Since no major objections were received, the SVD-WG decided to accept the proposal on October 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<code class="spot1">=</code>, m.15366<code class="spot1">=</code>, c.1823<code class="spot1">=</code>, n.611<code class="spot1">=</code>, r.377<code class="spot1">=</code>, p.Val76<code class="spot1">=</code>. 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 nucleotides were 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 (an 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, including UTRs) 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: the description of the variant on DNA level is mandatory.

protein#

  • LRG_199p1:p.(Phe41=)   (LRG_199t1:c.123C>T)
    the predicted consequence of variant c.123C>T (on DNA level) is that amino acid residue 41 is an Arg, like in the protein reference sequence (the amino acid was not changed, RNA was not analysed).
    NOTE: the description of the variant on DNA level is mandatory (depending on the amino acid, up to 5 different DNA changes may leave the amino acid unchanged).