Checklist for the description of sequence
Last modified April 28, 2014
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Going through publications one can easily see where people tend to offend
the "Current recommendations for the
description of sequence variants". The checklist below
covers the most problematic issues and should assist those preparing a
publication to describe sequence variants following the current
- Reference Sequence - do you clearly mention the
reference sequence used for numbering (nucleotides/amino acids)?
A publication should mention, preferably in the Materials & Methods
section and/or Table legend, which sequence file was used as reference
sequence for numbering of the residues (DNA, RNA and protein) and
describing the variants; see Recommendations,
Discussion and mtDNA
- do you mention a GenBank (not GeneBank)
RefSeq-file accession number with version number?; do
not forget the underscore in the accession number (correct is NM_004006.2,
- a genomic reference sequence starts with nucleotide 1; a genomic
reference sequence can not have negative numbers
- for a coding DNA reference sequence, do you clearly state that nucleotide
numbering uses the A of the ATG translation initiation start site
as nucleotide 1?
- when you do
not use a coding DNA reference sequence and do
not start nucleotide numbering with 1 at the A
of the ATG translation initiation start you should
not use descriptions preceded by "c.".
- if legacy numbering is used, this can only be done in
addition to the approved nomenclature.
- does your reference sequence contain introns?; not that NM_
reference sequences cover mature transcripts and do not contain
- Intronic variants - do you indicate where the reference
intron sequence can be found ?
The recommendation is to describe intronic variants in
the format "c.89-2A>G" and not like "IVS4-2A>G"
(see Discussion). When the format "IVS4-2A>G"
is used, it is essential to give a clear reference for intron
/ exon numbering and to mention the reference
sequence used for the intron.
- Tabular overview - do you provide a clear,
unequivocal overview of all changes reported?
Preferably, a publication contains a tabular overview of all
variants reported. This overview contains columns describing the change
at DNA-level (absolutely essential) and, optional, at RNA
and protein level. When data on RNA and/or protein
level are provided, it should be made clear whether the data were deduced
or experimentally verified (i.e. state explicitly when
RNA was analysed, e.g. to study the consequences of a variant affecting
- are insertions reported in the format c.51_52insT?
Since it is not clear whether one means insertion at or
insertion after position 52, insertions should not
be reported as c.52insT but in the format c.51_52insT (see Discussion).
- do you give the inserted sequence?
Describing a variant like c.5439_430ins6 is not
sufficient, the inserted sequence (ins6, e.g.
TGCCAT) should always be mentioned.
- are the insertions reported really insertions or are they in fact
Duplicating insertions should be described as duplications, not as
insertions; for the change CCAGTAAC to CCAGTGTAAC
the description is c.4_5dup (or c.4_5dupGT) is correct, c.5_6insGT
is not correct (see Discussion).
- Most 3' position - do you correctly assign the change to the
most 3' (or C-terminal for protein variants) position possible?
For deletions, duplications and insertions the most 3'
position possible is arbitrarily assigned to have been
changed (see Recommendations);
important especially in single residue (nucleotide or amino acid)
stretches or tandem repeats. Example CCAGTGTAAC
to CCAGTAAC is described as c.6_7del (or c.6_7delGT, not as c.3_4del or
- Recessive diseases - do you clearly describe which
changes are found in which combination?
a publication describing sequence changes found in patients suffering
from a recessive disease should for each patient explicitly mention
which combination of changes was identified
(see Recommendations). Example
c.[76C>T];[87G>A] or c.[76C>T];[?].
NOTE: this description differs from
that describing several changes in one allele, which
has the format c.[76A>C;113G>C].
- Range - the sign used to indicate a range is "_"
(underscore) and not a "-" (minus)?
To prevent confusion, the underscore
should be used to indicate a range
and not the minus sign. The minus
sign should only be used to indicate negative
numbers. The correct description to indicate a deletion of the
coding DNA nucleotides 12 to 14 is c.12_14del. Not correct is
c.12-14del, this describes a deletion of nucleotide -14 in the intron
directly preceding cDNA nucleotide 12 (see Discussion).
- Deletion - do you indicate the first and last residue involved
in a deletion?
A deletion of more than one residue should mention the first and last
residue deleted, separated using a "_" (underscore), e.g. c.21_24del or
p.Ala13_Gln16del. Descriptions like c.21del3 should not be used.
- Describe at DNA-level - do you describe all changes reported at
All changes reported must be described at DNA-level
- when descriptions at protein level are given in the text, upon
first appearance, use a format like "c.78G>C (p.(Trp26Cys),
RNA not analysed)" or "c.78G>C (p.Trp26Cys, RNA
- description of "silent variants" in the format
"p.(Leu54Leu) (or p.(L54L))" should not be used
(see Discussion). Descriptions
should be given at DNA level. Descriptions like p.(Leu54Leu) are
non-informative and not unequivocal (there are five possibilities at
DNA level); a correct description is c.162C>G
- RNA protein level descriptions
Recommendations exist to describe alternative transcripts deriving from
one allele (see Recommendations).
Since these descriptions may be rather complex to explain, it is wise to
include a link to the HGVS recommendations in the publication.
- Protein level descriptions
- protein reference sequence - the protein reference
sequence should represent the primary translation
product, not a processed mature protein, and thus include any signal
peptide sequences (see Recommendations).
/ * - do you use Ter or * to indicate a
translation stop codon; the X is not allowed anymore (see Important
- one/three letter amino acid code - are the correct
amino acid codes used at protein level?; several amino acids
start with the same initial letter (Ala, Arg, Asn, Asp start with A,
Gln, Glu, Gly with G, Leu, Lys with L,
Phe, Pro with P and Thr, Tyr with T)
but that initial letter is used as one-letter-amino-acid-code for
only one of these (see Discussion and
Codons and amino acids)
- initiating methionine (Met1) - p.Met1?
denotes that amino acid Methionine-1 (translation initiation site)
is changed and that it is unclear what the consequence of this
change is. When experimental data show that no protein is made, the
description p.0 should be used. The description p.Met1Val is
not allowed (see Discussion)
- no-stop change - recommendations have recently been
made to describe substitutions in the stop codon, so called no-stop
changes like p.*110Tyrext*16 (see Recommendations)
Do not describe polymorphic variants as c.127A/G (or p.43I/V). A
description of a variant should be neutral and
polymorphisms and pathogenic changes should not be described differently
(see Discussion). Correct
descriptions are c.127A>G and p.(Ile43Val).
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