Add note about grpmax

browser/help/helpPageTableOfContents.ts

@@ -11,6 +11,7 @@ const helpPageTableOfContents: { topics: string[]; faq: FaqTopic[] } = {
     'relatedness-filtering',
     'vep',
     'faf',
+    'grpmax',
     'constraint',
     'pext',
     'regional-constraint',

browser/help/topics/faf.md

@@ -5,14 +5,8 @@ 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.
 
-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**.
+Note that the GroupMax FAF 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**.
 
 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 **AF**.
-
-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.
+On the browser, the **GroupMax FAF** annotation is directly available on the variant page. In the VCF and Hail Tables, the filtering allele frequency annotation (abbreviated "`faf`") is computed globally and for each genetic ancestry group. Filtering allele frequencies (FAFs) for each genetic ancestry group are listed separately with 95% and 99% CIs.

browser/help/topics/grpmax.md

@@ -0,0 +1,8 @@
+---
+id: grpmax
+title: '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 **AF**. Note that `grpmax` is distinct from filtering allele frequency.
+
+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.

browser/src/help/__snapshots__/HelpPage.spec.tsx.snap

@@ -688,6 +688,15 @@ exports[`Help Page has no unexpected changes 1`] = `
           faf
         </a>
       </li>
+      <li>
+        <a
+          className="-Link c3"
+          href="/help/grpmax"
+          onClick={[Function]}
+        >
+          grpmax
+        </a>
+      </li>
       <li>
         <a
           className="-Link c3"
@@ -943,6 +952,17 @@ exports[`Help Page has no unexpected changes 1`] = `
               faf
             </a>
           </li>
+          <li
+            className="c10"
+          >
+            <a
+              className="-Link c3"
+              href="/help/grpmax"
+              onClick={[Function]}
+            >
+              grpmax
+            </a>
+          </li>
           <li
             className="c10"
           >