On the Disease and Population reference tracks, Affected AF and Background AF are pooled across contributing cohort arms (sum of allele counts divided by sum of allele numbers), not the maximum across arms, so the displayed frequency matches the carrier-count scale and a small cohort with a high local frequency does not dominate the value. See the "Pooled allele frequency" section on each combined track's description page for which cohorts contribute to the pool numerator and denominator.
All three combined tracks share the same Consequence filter (Missense, Synonymous, Stop
Gained, Frameshift, Splice Donor, Splice Acceptor, Intron, 3' UTR, 5' UTR, Non-coding,
-Intergenic, Other). The filter uses OR logic across the comma-separated consequence tokens
+Intergenic, Other). The filter uses OR logic across the comma-separated consequence terms
on each variant: a variant tagged stop_gained,frameshift is selected by either
the "Stop Gained" or the "Frameshift" filter. The "Other"
bucket catches the less common
Sequence Ontology consequence
that don't fit the named buckets above. Examples
include splice_region (variant near a splice site but outside the canonical
donor/acceptor), start_lost / stop_lost (variant disrupts the
start codon or replaces the stop codon with a coding amino acid),
stop_retained (variant changes the stop codon but keeps it a stop),
inframe_insertion / inframe_deletion (in-frame indel that adds or
removes whole codons), and coding_sequence (CDS variant where the precise
impact is undetermined). If you include "Other" in the filter selection, no
records will be hidden by the consequence filter.