Older versions
-
Version 20.05
Accepted proposals include SVD-WG007 and SVD-WG008:- SVD-WG008 (Reference Sequences): specifies requirements for acceptable Reference Sequences.
- SVD-WG007 (RNA fusion): specifies how to describe adjoined transcripts from gene fusions.
-
Version 19.01
Accepted proposals include SVD-WG005 and SVD-WG006:- SVD-WG006 (circular DNA): allows descriptions like
o.16000_100del
. - SVD-WG005 (gom/lom): allows descriptions of changes in general methylation status, like
g.123_456|lom
. - Named extension ISCN: Proposal SVD-WG004 (ISCN<>HGVS) has been accepted a "named extension ISCN".
- SVD-WG006 (circular DNA): allows descriptions like
-
Version 15.11
Accepted proposals include SVD-WG001 and SVD-WG002:- SVD-WG001 (no change): allows descriptions like
g.11890634G=
,c.123G=
,r.123g=
, andp.(Arg41=)
. - SVD-WG002 (n. reference sequence): allows descriptions like
NR_028379.1:n.345A>G
. - HGVS nomenclature version 15.11 is described in Den Dunnen et al. (2016) HGVS recommendations for the description of sequence variants: 2016 update. Hum.Mutat. 25: 37: 564-569. The most significant changes between version 15.11 and version 1.0 are described below.
- SVD-WG001 (no change): allows descriptions like
-
Version 2.121101
- Variants affecting translation termination
Variants that replace the translation termination codon but do not encounter a new stop in the new reading frame are described asp.321Argext?
.
Frameshift variants with the same effect are described asp.Ile321Argfs*?
(see Protein descriptions).
- Variants affecting translation termination
-
Version 2.120831
- Protein description in parentheses
Parentheses in protein variant descriptions can be omitted when there is sufficient experimental evidence. - Variants affecting translation initiation
on protein level, variants that generate a new upstream translation initiation codons are described using the formatp.Met1ext-5
(see Protein extensions).
- Protein description in parentheses
-
Version 1
The 2000 publication of Den Dunnen JT and Antonarakis SE (Mutation nomenclature extensions and suggestions to describe complex mutations: a discussion. Hum.Mutat. 15:7-12) contains a more formal set of recommendations and is considered as version 1. -
Version 0
On the page "History regarding the description of sequence variants" we give an overview of all publications on the description of sequence variants. These papers can be considered as pre-versions of the first recommendations, a version 0.
Changes/additions going from the 2000 to 2016 recommendations#
-
Reference sequence
for diagnostic applications, the recommendation is to use a Locus Reference Genomic sequence (LRG, Dalgleish et al. 2010) as the reference sequence for variant descriptions. Prefixes for new reference sequence types have been added (e.g., m. and n., as well as indicators to specify different transcript variants (t1) and protein isoforms (p1) annotated in the reference sequence (see Reference Sequences). -
Definitions
the basic types of variants were defined more strictly. In addition, variant types have been prioritized (see General recommendations). -
Pre-existing standards
pre-existing standards from the IUPAC and IUBMB for the description of nucleotides and amino acids are now used throughout the recommendations. These include letter codes to describe incompletely specified residues at both DNA and protein level (see Standards). Description of the translation termination (stop) codon on the protein/amino acid level changed from "X" to "Ter" / "*" since "X" in the IUPAC-IUB nomenclature means an "unspecified" or "unknown" amino acid. -
Incorporate ISCN standards
recommendations were made to describe changes with uncertain break points (i.e. not sequenced), obtained using technologies like FISH, arrays and MLPA. Furthermore, where possible, HGVS incorporated established ISCN standards in the recommendations, include the use of/
(forward slash) to describe somatic variants and//
for chimerism (see General recommendations). -
Simplification
in HGVS version 1.0, some symbols were used for more than one purpose leading to undesired confusion. These inconsistencies were removed. -
Prediction / experimental proof
to clarify a variant described on the protein level is a prediction, without experimental evidence, the recommendation was added to describe the predicted consequence in parentheses, likep.(Arg12Gly)
. -
Repeated sequences
recommendations were made to describe variability in repeated sequences (mono-, di-, tri- residue stretches, etc. (see Repeated sequences).