# What is the Variant\_annotation column and how is function of mutations annotated?

**URL:** <https://forum.depmap.org/t/what-is-the-variant-annotation-column-and-how-is-function-of-mutations-annotated/105>\
**Category:** Q&A\
**Tags:** portal, omics\
**Created:** [July 27, 2020, 2:44pm UTC](https://forum.depmap.org/t/what-is-the-variant-annotation-column-and-how-is-function-of-mutations-annotated/105 "2020-07-27T14:44:20Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![jnoorbak](https://yyz1.discourse-cdn.com/flex035/user_avatar/forum.depmap.org/jnoorbak/32/12_2.png) [@jnoorbak](https://forum.depmap.org/u/jnoorbak)\
**Post date:** [July 27, 2020, 2:44pm UTC](https://forum.depmap.org/t/what-is-the-variant-annotation-column-and-how-is-function-of-mutations-annotated/105/1 "2020-07-27T14:44:20Z")

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Users have asked us:

What is the Variant\_annotation column in CCLE\_mutations.csv, and how are mutations shown in the portal?

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<div class="post-metadata">

**Author:** ![jnoorbak](https://yyz1.discourse-cdn.com/flex035/user_avatar/forum.depmap.org/jnoorbak/32/12_2.png) [@jnoorbak](https://forum.depmap.org/u/jnoorbak)\
**Post date:** [July 27, 2020, 2:44pm UTC](https://forum.depmap.org/t/what-is-the-variant-annotation-column-and-how-is-function-of-mutations-annotated/105/2 "2020-07-27T14:44:47Z")

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#### Which tool is used to annotate mutations?

We use Oncotator to annotate the mutations. The output of this tool is stored in the ‘Variant\_Classification’ column of the mutation maf file

#### The Variant\_annotation column in the CCLE\_mutations.csv MAF file

We have added a Variant\_annotation column in the [DepMap mutation data, CCLE\_mutations.csv](https://depmap.org/portal/download/), which groups mutations using more inclusive definitions. The Variant\_annotation column labels a mutation as “damaging”, “other non-conserving”, “other conserving” or “silent” using the Variant\_Classification column and the definitions below. “Hotspot” is not a label in Variant\_annotation, but can be obtained from the isTCGAhotspot and isCOSMIChotspot columns.

#### Coloring mutations in portal visualizations

The portal colors mutations with the priority order of hotspot \> damaging \> other non-conserving \> other conserving. For instance, if a gene in a cell line has both hotspot and damaging mutations, it will be colored as hotspot. Silent mutations are not colored. These mutation categories are defined below. An example of this coloring scheme can be found [here](https://depmap.org/portal/gene/BRCA1?tab=dependency&characterization=mutation) and in the following legend:  
 ![Screen Shot 2020-07-27 at 11.24.18 AM](https://canada1.discourse-cdn.com/flex035/uploads/depmap/original/1X/07fd165a8d2b6ba2ba812c61f66208524af89a87.png)

The mutation dataset is also available to plot as 0 or 1 on an axis in [data explorer](https://depmap.org/portal/interactive/) in cases such as [grouping by Mutation](https://depmap.org/portal/interactive/?filter=&regressionLine=false&associationTable=false&x=slice%2FAvana%2F2475%2Fentity_id&y=&color=slice%2Fmutation%2FBRAF%2Flabel). Note that this uses a binarized defintion of mutation, which includes any “hotspot”, “damaging”, or “other non-conserving” mutation.

#### Hotspot

- Is a hotspot in TCGA
- Is a hotspot in COSMIC
- Is not silent

#### Damaging

- Start\_Codon\_SNP
- Start\_Codon\_Del
- Start\_Codon\_Ins
- Splice\_Site
- Frame\_Shift\_Del
- Frame\_Shift\_Ins
- Nonsense\_Mutation
- De\_novo\_Start\_OutOfFrame

#### Other non-conserving

- Missense\_Mutation
- In\_Frame\_Del
- In\_Frame\_Ins
- Nonstop\_Mutation
- Stop\_Codon\_Del
- Stop\_Codon\_Ins

#### Other conserving

- 5’Flank
- Intron
- IGR
- 3’UTR
- 5’UTR

#### Silent

- Silent