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Update FAF help page #1276

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Nov 13, 2023
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Update FAF help page #1276

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ed1a515
Updated FAF to make it clearer that this field contains information a…
ch-kr Nov 8, 2023
0113054
Update browser/help/topics/faf.md
ch-kr Nov 13, 2023
edb4a57
Update browser/help/topics/faf.md
ch-kr Nov 13, 2023
54d173b
move note about faf, also update grpmax to be about grpmax
ch-kr Nov 13, 2023
b499386
Update browser/help/topics/faf.md
ch-kr Nov 13, 2023
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10 changes: 6 additions & 4 deletions browser/help/topics/faf.md
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Expand Up @@ -5,12 +5,14 @@ title: 'Filtering allele frequency'

This annotation can be used for filtering variants by allele frequency against a disease-specific threshold that can be set for each disease (e.g. BA1 in the 2015 ACMG/AMP guidelines). In this case the filtering allele frequency (FAF) is the maximum credible genetic ancestry group AF (e.g. the lower bound of the 95% confidence interval (CI)). If the FAF is above the disease-specific threshold, then the observed AC is not compatible with pathogenicity. See http://cardiodb.org/allelefrequencyapp/ and [Whiffin _et al._ 2017](https://www.nature.com/articles/gim201726) for additional information.

This calculation only includes non-bottlenecked genetic ancestry groups: we did not calculate this metric on the Amish (`ami`), Ashkenazi Jewish (`asj`), European Finnish (`fin`), Middle Eastern (`mid`), and "Remaining Individuals (`rmi`) groups.
Note that this annotation contains filtering allele frequency information from the genetic ancestry group with the highest **FAF**, not the filtering allele frequency information calculated on the genetic ancestry group with the highest **AF**.

On the browser, this annotation is directly available on the variant page. In the VCF and Hail Tables, this annotation is computed globally and for each genetic ancestry group. Genetic ancestry group specific AFs are listed separately with 95% and 99% CIs.
The filtering allele frequency calculation only includes non-bottlenecked genetic ancestry groups: we did not calculate this metric on the Amish (`ami`), Ashkenazi Jewish (`asj`), European Finnish (`fin`), Middle Eastern (`mid`), and "Remaining Individuals" (`rmi`) groups.

On the browser, this annotation is directly available on the variant page. In the VCF and Hail Tables, this annotation (abbreviated "`faf`") is computed globally and for each genetic ancestry group. Filtering allele frequencies (FAFs) for each genetic ancestry group specific are listed separately with 95% and 99% CIs.

### <a name="grpmax"></a>Group maximum allele frequency

This annotation (abbreviated "`grpmax`") contains allele frequency information (AC, AN, AF, homozygote count) for the non-bottlenecked genetic ancestry groups with the highest frequency.
This annotation (abbreviated "`grpmax`") contains allele frequency information (AC, AN, AF, homozygote count) for the non-bottlenecked genetic ancestry groups with the highest **AF**.

For gnomAD v4, this excludes Amish (`ami`), Ashkenazi Jewish (`asj`), European Finnish (`fin`), Middle Eastern (mid), and "Remaining Individuals" (`rmi`) groups. For gnomAD v2, this excludes Ashkenazi Jewish (`asj`), European Finnish (`fin`), and "Remaining Individuals" (`rmi`) groups.
For gnomAD v4, this calculation excludes Amish (`ami`), Ashkenazi Jewish (`asj`), European Finnish (`fin`), Middle Eastern (`mid`), and "Remaining Individuals" (`rmi`) groups. For gnomAD v2, this calculation excludes Ashkenazi Jewish (`asj`), European Finnish (`fin`), and "Remaining Individuals" (`rmi`) groups.
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