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/varFreqsAffected.html src/hg/makeDb/trackDb/human/varFreqsAffected.html
index 53bec716f0a..e1cd9bbefab 100644
--- src/hg/makeDb/trackDb/human/varFreqsAffected.html
+++ src/hg/makeDb/trackDb/human/varFreqsAffected.html
@@ -39,31 +39,33 @@
     <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 affected/case allele frequency times 1000.
 </p>
 
 <h3>Pooled allele frequency</h3>
 <p>
 <b>Affected AF</b> is the pooled rate across contributing affected arms:
 <code>affectedAF = sum(AC) / sum(AN)</code>, where <b>affectedAC</b> sums the allele counts
 and <b>affectedAN</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>). Cohorts that publish only AF
-contribute via a configured <code>default_an</code> in the build configuration. Cohorts
+(with no AC or AN of their own) 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 and have no <code>default_an</code> set (currently GREGoR's per-arm
 AC_AFFECTED/UNAFFECTED/UNKNOWN) are listed in <b>affectedCohorts</b> but do not contribute
 to the pool numerator or denominator; their carriers are visible in the per-database AC
 column instead. The pooled rate is preferred over a max-across-cohorts statistic so a
 small cohort with a high local AF cannot dominate the displayed frequency.
 </p>
 
 <h3>Finding case-enriched loss-of-function variants</h3>
 <p>
 To look for protein-truncating variants that are common in affected individuals but rare
 in the background, set the Consequence filter to Stop Gained, Frameshift, Splice Donor and
 Splice Acceptor (these appear red), then add an upper limit on the
 <b>Background AF</b> filter. Each variant here carries both its affected frequency and its
 background frequency, so this isolates variants seen in cases with little or no presence in
 the population/unaffected set. Comparing visually against the