Nomenclature

Laboratories use a common nomenclature system to identify variants. In this resource, the elements of that system are explained.

Common Notations and Abbreviations

General  
SNV Single nucleotide variant
CNV Copy number variant
Location  
c. Coding DNA reference sequence
n. Non-coding DNA reference sequence
Functional impact  
p. Protein change
Nucleotide change types  
> Substitution
Del Deletion
Dup Duplication
Ins Insertion
Inv Inversion
Fs Frame shift

 

Variant Types

Nucleotide Variants

DNA Sequence Nomeclature Meaning
T C G T G T A   Reference DNA sequence
T C G C G T A c.4T>C SNV - Single Nucleotide Variant
T C G T A G T A c.4_4insA Insertion
T C G _ G T A c.4delT Deletion
T C G C C G _ G T A c.4delinsCCG Indel - insertion and deletion
T C G C G T G T A c.4_5dupCG Duplication

Other Variant Types


Variant Type Nomenclature Meaning
Copy number variant Amplification (amp) Section of DNA repeated
  Deletion (del) Section of DNA deleted
Rearrangement Fusion 2 genes broken and re-attached together, which can activate oncogenes

Terminology

Variant refers to any difference in the DNA sequence compared to a reference genome. Variants may or may not have an impact on the function of the gene.

  • Benign or likely benign variants do not have any functional consequences and are often seen commonly in the general population. You may also see these referred to as “polymorphisms.”
  • Pathogenic or likely pathogenic variants impact the function of the gene in some way. Most accurately, these are referred to as “variants that impact function”. More commonly, these may be referred to as “mutations.”
  • Variants of unknown significance or VUS are changes in the gene for which the impact is unknown. This may be because they are rare and there is not enough data available to be conclusive about their functional impact. Over time, VUS are likely to be re-classified as benign or pathogenic as more data are amassed.

Copy number variation is when a section of DNA is repeated or a section of repetitious DNA is deleted.

Functional Impact of Sequence Variants

Functional Impact Meaning Example
Silent Variant does not change amino acid/protein and is unlikely to affect function

CGT to CGC

Arginine to Arginine

Missense Variant changes amino acid

GTA to GAA

Valine to Glutamic Acid

Nonsense Variant changes amino acid to stop codon

TCA to TAA

Serine to stop