Laboratories use a common nomenclature system to identify variants. In this resource, the elements of that system are explained.
Common Notations and Abbreviations
|SNV||Single nucleotide variant|
|CNV||Copy number variant|
|c.||Coding DNA reference sequence|
|n.||Non-coding DNA reference sequence|
|Nucleotide change types|
|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
|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|
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
|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