> For the complete documentation index, see [llms.txt](https://help.bioinsight.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.bioinsight.illumina.com/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/workbench-and-pipeline/gnomad-annotation-v100.41+.md).

# gnomAD Annotation (v100.41+)

GRCh37 cases use gnomAD v2.1 for population data annotation, while GRCh38 cases use gnomAD v4.1, available as Non-UKB and All datasets.

Use the **gnomAD Annotation** card to select the gnomAD v4.1 population dataset used for SNV annotation in GRCh38 cases.

## gnomAD v4.1 annotation datasets

The selected dataset annotates SNVs with **Total AF**, **Allele count**, **Hom/Hemi count**, **Max AF**.

The metrics are available on the [**Variant page**](/emedgene/emedgene-analyze-manual/variant_page/variant_page.md), as [**Variant table**](https://help.bioinsight.illumina.com/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/workbench-and-pipeline/pages/vpEMCVyDac5LYh1zxE6s#id-5.-population-frequency-data) columns, in [**Polymorphism filters**](/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab-beta-v100.39.0+/filters_presets_panel/filters/quick-filters/polymorphism_filters.md), [**Query Builder**](/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab-beta-v100.39.0+/filters_presets_panel/filters/query-builder-v100.40+.md), and in [exports](/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab-beta-v100.39.0+/variant_table/download_variants.md).

**gnomAD 4.1 Non-UKB**

* Excludes UK Biobank samples, helping reduce population bias.
* This is the default option.

**gnomAD 4.1 All**

* Includes UK Biobank samples, providing a larger sample size for allele-frequency calculations.
* Annotation with the **gnomAD 4.1 All** dataset includes the additional **gnomAD Grpmax FAF (95% CI)** metric on the [**Variant page**](/emedgene/emedgene-analyze-manual/variant_page/variant_page.md), as a [**Variant table**](https://help.bioinsight.illumina.com/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/workbench-and-pipeline/pages/vpEMCVyDac5LYh1zxE6s#id-5.-population-frequency-data) column, in [**Query Builder**](/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab-beta-v100.39.0+/filters_presets_panel/filters/query-builder-v100.40+.md), and in [exports](/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab-beta-v100.39.0+/variant_table/download_variants.md).

The **Versions** tab shows the dataset used for each case.

## Change the gnomAD annotation dataset

<figure><img src="https://1131024994-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGCW0DnLlE7QjoZPNmKIi%2Fuploads%2Fgit-blob-3685ad11283fe29310cd5b71e122723789e6fce7%2Fgnomad%20annotation.gif?alt=media" alt=""><figcaption><p>Selecting the gnomAD dataset for small variant annotation in GRCh38 cases.</p></figcaption></figure>

**Prerequisites:**

* Your pipeline version is v100.41 or later.
* You have the required [permissions](/emedgene/emedgene-analyze-manual/settings/user_roles/iam-scopes-emedgene-roles.md).

{% stepper %}
{% step %}
In the **gnomAD Annotation card**, select **gnomAD 4.1 Non-UKB** or **gnomAD 4.1 All**.
{% endstep %}

{% step %}
Select **Save** to confirm your choice.
{% endstep %}
{% endstepper %}

**Results:**

* Cases run after the change use the new dataset.
* Cases started before the change retain their original annotations until reanalysis.
* The organization activity log records the change.


---

# Agent Instructions
This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com.

## Querying This Documentation
If you need additional information that is not directly available in this page, you can query the documentation by asking a question.

Perform an HTTP GET request on the following URL with the `ask` and `goal` query parameters:

```
GET https://help.bioinsight.illumina.com/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/workbench-and-pipeline/gnomad-annotation-v100.41+.md?ask=<question>&goal=<user_goal>
```

`ask` is the immediate question: it should be specific, self-contained, and written in natural language.
`goal` is what the user is ultimately trying to achieve, the reason they need the answer. Sharing it helps GitBook give you a better, more relevant answer. A goal is most helpful when it describes the outcome the user wants rather than restating the question. For example, with `ask=how do I create an API token`, a goal like `automate deployments from our CI pipeline` lets GitBook tailor the answer to that use case.

The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.
