> For the complete documentation index, see [llms.txt](https://docs.omics.ai/products/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.omics.ai/products/workbench/variant-interpreter/reviewing-variants/copy-number.md).

# Copy number

Copy-number variants (CNVs) are changes in the number of copies of a region: losses (deletions) and gains (duplications). The Copy Number tab presents the CNV calls with visualizations built for dosage review.

## Visualizations

* **Scatter plot**: a genome-wide view of the copy-number calls.
* **Ideogram**: the calls arranged across the chromosomes. Click directly on the visualization to open a slide-out panel for the selected gene.

Calls are **colour-coded** for deletions and duplications, and for their classification (likely pathogenic, uncertain, or likely benign).

{% hint style="info" %}
A **gene dosage matrix** is also part of this tab. It does not yet have a visualization; this page will be updated when it ships.
{% endhint %}

## The candidate table

Each row is a genotyped copy-number variant. You can search, sort, filter, and customize the columns in the table using the **Columns** dropdown.

The default columns in the candidate table include:

| Column                       | Description                                                                                                                       |
| ---------------------------- | --------------------------------------------------------------------------------------------------------------------------------- |
| **User Classification**      | The classification manually assigned to the copy-number variant by a reviewer (e.g., Pathogenic, Likely Pathogenic, VUS, Benign). |
| **Automated Classification** | The automated classification generated by the system's pipeline rules or algorithms.                                              |
| **AnnotSV Score**            | The pathogenicity annotation score or class assigned by AnnotSV.                                                                  |
| **SV Type**                  | The type of copy-number variant (e.g., `DEL` (deletion/loss), `DUP` (duplication/gain)).                                          |
| **Chrom**                    | The chromosome where the copy-number variant is located.                                                                          |
| **Pos**                      | The starting genomic coordinate of the copy-number variant.                                                                       |
| **End Position**             | The ending genomic coordinate of the copy-number variant.                                                                         |
| **Genes**                    | Standard gene symbols of the genes overlapped or affected by the copy-number variant.                                             |
| **SV Length**                | The length of the copy-number variant in base pairs.                                                                              |
| **Filter Status**            | The filter status of the variant call from the caller (e.g., `PASS` or specific filtering flags).                                 |

## Filters

The filter drawer offers:

* **User Classification**: Pathogenic, Likely Pathogenic, VUS, Likely Benign, Benign.
* **Type**: DEL (loss) or DUP (gain).
* **Gene**: filter by gene symbol.
* **Chromosome**: chr1 to chr22, chrX, chrY.
* **Copy Number**: an integer copy-number range.
* **Position**: a genomic-coordinate range.

## How to review

1. Scan the scatter and ideogram views for calls flagged as likely pathogenic.
2. Click a call to open its detail panel and review the affected genes and dosage change (loss vs gain).
3. Classify and add findings to the [report](/products/workbench/variant-interpreter/generating-a-report.md).


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