1259dcfba3a263d92d2602665fd866dc44b47996
lrnassar
  Sun Jun 21 11:17:10 2026 -0700
Clarify varFreqs description page wording per code review feedback. refs #37733

Reword the default_an sentence in the Pooled allele frequency sections of
varFreqsAffected.html and varFreqsBackground.html to explain that cohorts
publishing only AF are pooled via an assigned default_an, with per-arm AC
derived as round(AF * default_an). Change "tokens" to "terms" in the
Consequence filter section of varFreqs.html.

diff --git src/hg/makeDb/trackDb/human/varFreqsBackground.html src/hg/makeDb/trackDb/human/varFreqsBackground.html
index 2b7d13f8ecb..5d2f82eb6ef 100644
--- src/hg/makeDb/trackDb/human/varFreqsBackground.html
+++ src/hg/makeDb/trackDb/human/varFreqsBackground.html
@@ -36,32 +36,34 @@
     <td>synonymous, stop_retained</td></tr>
 <tr><th style="background-color:#808080;width:2em">&nbsp;</th>
     <td>Non-coding / intergenic</td>
     <td>intron, non_coding, intergenic, UTR</td></tr>
 </table>
 <p>
 The score (used for shading) is the pooled background allele frequency times 1000.
 </p>
 
 <h3>Pooled allele frequency</h3>
 <p>
 <b>Background AF</b> is the pooled rate across contributing population cohorts and
 unaffected/control arms: <code>backgroundAF = sum(AC) / sum(AN)</code>, where
 <b>backgroundAC</b> sums the allele counts and <b>backgroundAN</b> sums the allele
 numbers across each cohort/arm that provides both AC and AF (the per-arm AN is derived as
-<code>round(AC / AF)</code>). Two cohorts that publish only AF (ABraOM, ALFA) contribute
-via a configured <code>default_an</code> in the build configuration. Cohorts that publish
+<code>round(AC / AF)</code>). Two cohorts that publish only AF (ABraOM, ALFA) are still
+pooled by assigning them an assumed allele number, set as a <code>default_an</code> in the
+build configuration; their per-arm AC is then derived as <code>round(AF &times; default_an)</code>.
+Cohorts that publish
 only AC with no <code>default_an</code> set (currently MGRB and the GREGoR unaffected and
 unknown arms), and cohorts that contribute only through per-population AC/AF (currently
 AllOfUs), are listed in <b>backgroundSources</b> but do not contribute to the pool
 numerator or denominator; their data remain visible in the per-database and per-population
 AC/AF columns. The pooled rate is preferred over a max-across-cohorts statistic so a small
 cohort with a high local AF (for example AllOfUs Oceanian) cannot dominate the displayed
 frequency.
 </p>
 
 <h2>Filters</h2>
 <ul>
   <li><b>Variant Type</b> and <b>Consequence</b>: restrict to SNV/insertion/deletion/MNV
       and to predicted consequence classes (the Consequence filter uses OR logic over the
       comma-separated tokens on each variant).</li>
   <li><b>Background AF</b>, <b>AC</b>, <b>AN</b>: the pooled allele frequency