# Custom Annotations

Custom Annotations allow you to annotate custom attributes (labels, scores, and population frequency) to variants or variants within a genomic region.

## Create a new Custom Annotation file

1. Select the [Configuration](/connected-insights/configure/configuration.md) icon (gear icon) in the top right area of the screen.
2. Select the **Test Components** tab.
3. Navigate to **Custom Annotations.**
4. Select **New**.
5. Download the **attached template.**
6. Edit the file with the desired annotations. Refer to [Custom Annotation File Format](https://illumina.github.io/IlluminaConnectedAnnotationsDocumentation/file-formats/custom-annotations/).

The supported data categories for custom annotation in Connected Insights are as follows:

* Filter: String labels
* Score: Numeric values
* AlleleFrequency: Allele frequency for population frequency data

## Upload a new Custom Annotation file

1. Select the [Configuration](/connected-insights/configure/configuration.md) icon (gear icon) in the top right area of the screen.
2. Select the **Test Components** tab.
3. Navigate to **Custom Annotations.**
4. Select **New**.
5. Upload the file.

## Download an existing Custom Annotation file

1. On the top toolbar, select **Configuration**, and then select the **Test Components** tab.
2. Select the **Custom Annotations** section.
3. Select the desired custom annotation.
4. Select **Download**.

## Annotating Variants

After a custom annotation is added to a [Test Definition](/connected-insights/configure/configuration/c-test-definition-setup.md) and cases are ingested using the test definition, the variants will be annotated. The annotations can then be [viewed](/connected-insights/interpret-and-report/inter-variant-grid/inter-modify-variant-grid.md) and [filtered ](/connected-insights/interpret-and-report/inter-variant-grid/avf-introduction/avf-variant-details-filters.md#custom-annotations)on.

When matching annotations for large variants (structural variants and copy number variants), by default Annotation Overlap (measured as the total overlap divided by the length of the annotation) of >= 0.75 is used, but can be changed to Reciprocal Overlap (measured as the total overlap divided by either the length of the annotation or the length of the variant, whichever is larger) by specifying *Reciprocal Overlap* in the **Description** column for the annotation. For more information, refer to [Custom Annotation File Format](https://illumina.github.io/IlluminaConnectedAnnotationsDocumentation/file-formats/custom-annotations/).


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