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, as Variant table columns, in Polymorphism filters, Query builder, and in exports.

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, as a Variant table column, in Query builder, and in exports.

The Versions tab shows the dataset used for each case.

Change the gnomAD annotation dataset

Selecting the gnomAD dataset for small variant annotation in GRCh38 cases.

Before you begin

• Your pipeline version is v100.41 or later.
• You have the required permissions.

1

In the gnomAD Annotation card, select gnomAD 4.1 Non-UKB or gnomAD 4.1 All.

2

Select Save to confirm your choice.

Result

• 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.