Going through publications one can easily see where people give variant descriptions that do not correctly follow HGVS nomenclature. The checklist below covers the most frequently offended rules. Going through should assist you while preparing a publication containing sequence variant descriptions.
- 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 Figure or Table legend, which reference sequence file was used to describe variants and for numbering of the residues (DNA, RNA and protein (see Reference Sequences)).
- do you mention a GenBank (not GeneBank) RefSeq-file with accession and version number ?; do not forget the underscore in the accession number (correct is NM_004006.2, not NM004006.2).
- genomic (g.) reference sequences start with nucleotide 1 and can not have nucleotides with additions like a +, - or *.
- for a coding DNA reference sequence, do you clearly state that nucleotide numbering starts with the A of the ATG translation initiation site as nucleotide 1 ?
- legacy numbering is only allowed in addition to approved numbering
- does your reference sequence contain the residue that you describe as changed ?
- NOTE: NM_ reference sequences cover mature transcripts, do not contain intron and gene flanking sequences, and can only be used to describe variants in introns using a “c.” prefix when a genomic reference sequence is given on which the coding DNA reference sequence is annotated, e.g. “NC_000023.10(NM_004006.2):c.94-2A>G” or “LRG_199t1:c.94-2A>G” (see Reference Sequences)
- Intronic variants - are descriptions of intron variants correct and complete ?
- descriptions referring to exon or intron numbers instead of nucleotide positions, e.g.”c.IVS4-2A>G”, are not allowed.
- do you properly describe ranges in the introns ? The format c.123-65_123-50 is correct, the format c.123-65_-50 is not, it is incomplete.
- Insertions - are descriptions of insertions correct and complete (see Insertion)?
- insertions should be reported using the format c.51_52insT.
- The format c.52insT is incomplete and not allowed.
- do you give the inserted sequence?
- Describing a variant as c.5439_5430ins6 is not allowed, the inserted sequence (for ins6 e.g. “TGCCAT”) should be specified.
- is the insertion reported indeed an insertion or is it in fact a duplication?
- Duplicating insertions should be described as duplications, not as insertions (see Duplication).
- The 3’ rule - do you correctly apply the 3’ rule?
- For deletions, duplications and insertions the most 3’ position possible is arbitrarily assigned to have been changed (see General recommendations). This rule also applies to variants in single residue stretches (mono-nucleotide or amino acid) or tandem repeats.
- Range - the sign used to indicate a range is the “_” (underscore), not a “-“ (minus)?
The correct description to indicate a deletion of 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 5’ of nucleotide c.12 (see Numbering).
- Deletion - do you indicate the first and last residue involved in a deletion?
Descriptions like g.123del3 are not allowed, correct is g.123_125del (see Deletion).
- Describe always at DNA-level - do you describe all changes reported at DNA-level?
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.76G>T (p.(Gly26Cys), RNA not analysed)” or “c.76G>T (r.76g>u p.Gly26Cys)”
- RNA level descriptions
HGVS nomenclature includes recommendations for the description of changes detected at the RNA level (see Recommendations).
- several transcripts derived from one allele are described using the format r.[76a>c,73_88del] (see RNA)
- protein level descriptions
- the protein reference sequence should represent the primary translation product, not a processed mature protein, and thus include the starting Methionine and a signal peptide sequence
- the recommendation is to use three letter amino acid code (see Protein)
- “Ter” or “*” should be used to indicate a translation stop codon; the X should not be used (see Protein)
- predicted “silent” protein level variants are described as p.(Leu54=), not as p.Leu54Leu or p.54L/L).
- the description p.(Met1Val) is not allowed (see Protein)
- Mutation / polymorphism
Do not use the terms “mutation” or “polymorphism” (see General recommendations)
- “polymorphic” variants should not be described using the “/” (slash), describe them as normal variants like c.127A>G and p.(Ile43Val).
- Recessive diseases - do you clearly describe which changes are found in which combination?
A publication describing variants in patients suffering from a recessive phenotype should, for each individual, explicitly mention which variants were found and in which combination (per allele).
- Tabular overview - is the overview of all changes reported clear and complete?
- Preferably, a publication contains a tabular overview of all variants reported. This overview contains columns describing the change at the DNA-level (absolutely essential) and, optional, at the 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 splicing).
- Make sure predicted consequences at protein level are reported in parentheses, like p.(Arg123Ser).
13 Variant types
- When giving numbers regarding the types of variants identified do not mix numbers at DNA, RNA and protein level. Give numbers separately for DNA, RNA and protein. Where would you list a substitution at DNA level, giving a deletion at RNA level (since it affects splicing) and a frame shift at protein level?
Be careful when using the term “pathogenic” (see General recommendations). A variant in itself is not “pathogenic”, whether it can be causally related to a phenotype observed in a patient is determined by other factors.