About Variant Notation¶

The variant notation is a shorthand to make it faster to enter/display variants. It is made up of two forms: continuous, and multi-feature. Most people will be more familiar with the continuous notation. It is based on HGVS v15.11 and can be used to describe any variant that has only a single reference feature (i.e. KRAS). Multi-feature notation is required when one needs to describe any variant involving multiple reference features. This could be something like a gene fusion where the reference features might be EWSR1, and FLI1.

Warning

The notation examples included in this documentation do not necessarily represent actual mutations. While they are all valid syntax, no attempt has been made to check that the sequences given are correct

To make this more transparent to end users, we have provided a notation parser view as part of the GraphKB Client where any input notation may be tested to see how it would be decomposed by the GraphKB parser

variant parser gif

General Notation¶

Prefixes¶

Both forms of notation can be described as two breakpoints and an event type. Some may also include reference sequence and untemplated sequence descriptions. Additionally both forms will use a common prefix notation. These prefixes are described under coordinate systems

Variant Types¶

The expected variant types are given below. Some types are only applicable to certain coordinate systems (i.e. frameshifts are protein only).

Variant Type	Description	Standard HGVS	Prefix Specific
>	substitutions	✔	g / c / r / n
del	deletions	✔
delins	indels	✔
dup	duplications	✔
fs	frameshifts	✔	p
ext	extensions	✔	p
ins	insertions	✔
inv	inversions	✔
fusion	gene fusion
trans	translocation
itrans	inverted translocation
mut	non-specific mutation
spl	splice site mutation		p
mis	missense mutation		p

Unsupported HGVS Features¶

There are a few elements of the HGVS v15.11 notation that are not yet supported (contributions are welcome!). These include: