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Sex-Specific Allele Frequency

Scenario

You are analyzing a candidate X-linked recessive gene. A hemizygous variant in males may be pathogenic, but the same variant in females acts as a heterozygous carrier state. Allele frequency means something different for each sex due to ploidy, and a combined AF obscures the clinically relevant frequencies.

Why Standard Databases Fall Short

Most population databases report a single AF for chrX variants, combining diploid female calls and haploid male calls. This average is appropriate for some purposes but misleading for X-linked recessive analysis, where the male hemizygous frequency is the clinically relevant metric.

For a variant at chrX non-PAR with AC=10 in 500 males (AN=500) and AC=5 in 1000 females (AN=2000):

  • Male hemizygous rate: 10/500 = 2%
  • Female carrier rate: 5/2000 = 0.25%
  • Combined AF: 15/2500 = 0.6%

The combined AF (0.6%) obscures the fact that 2% of males are hemizygous carriers — a crucial number for X-linked recessive risk assessment.

Solution with AFQuery

AFQuery applies ploidy-aware AN computation automatically. For chrX non-PAR positions:

  • Males contribute AN=1 (haploid)
  • Females contribute AN=2 (diploid)

Using --sex male returns AF over a purely haploid denominator — the true hemizygous frequency. Using --sex female returns AF over the diploid denominator.

Computing Sex-Specific AF at chrX

1. Query full cohort (combined)

afquery query --db ./db/ --locus chrX:153296777

chrX:153296777 C>T  AC=15  AN=2500  AF=0.0060  n_eligible=1500  N_HET=5  N_HOM_ALT=0  N_HOM_REF=1495  N_FAIL=0

AN=2500: 500 males × 1 + 1000 females × 2 = 2500 (mixed ploidy)

2. Query males only (hemizygous frequency)

afquery query --db ./db/ --locus chrX:153296777 --sex male

chrX:153296777 C>T  AC=10  AN=500  AF=0.0200  n_eligible=500  N_HET=10  N_HOM_ALT=0  N_HOM_REF=490  N_FAIL=0

Hemizygous rate: 2% (N_HET here represents hemizygous males, GT=1)

3. Query females only (carrier frequency)

afquery query --db ./db/ --locus chrX:153296777 --sex female

chrX:153296777 C>T  AC=5  AN=2000  AF=0.0025  n_eligible=1000  N_HET=5  N_HOM_ALT=0  N_HOM_REF=995  N_FAIL=0

Carrier rate: 0.25%

4. Python API comparison

from afquery import Database

db = Database("./db/")

male = db.query("chrX", pos=153296777, sex="male")[0]
female = db.query("chrX", pos=153296777, sex="female")[0]
combined = db.query("chrX", pos=153296777)[0]

print(f"Male hemizygous rate:  {male.AF:.4f}  (AN={male.AN})")
print(f"Female carrier rate:   {female.AF:.4f}  (AN={female.AN})")
print(f"Combined AF:           {combined.AF:.4f}  (AN={combined.AN})")

5. Annotating with sex-stratified AF

# Annotate using only male samples (for X-linked recessive analysis)
afquery annotate \
  --db ./db/ \
  --input patient.vcf.gz \
  --output annotated_males.vcf.gz \
  --sex male

Biological Interpretation

Metric Value Clinical relevance
Male hemizygous rate 2% ACMG BS1 for X-linked recessive (exceeds 0.01 threshold)
Female carrier rate 0.25% Heterozygous carriers; does not inform X-linked recessive pathogenicity
Combined AF 0.6% Misleading for X-linked analysis — neither the hemizygous nor carrier rate

For X-linked recessive disorders, always use --sex male when evaluating the hemizygous carrier frequency.

PAR Regions

The Pseudoautosomal Regions (PAR1/PAR2) on chrX behave like autosomes. At PAR positions, males contribute AN=2 and sex-stratified queries are less meaningful. AFQuery applies the correct PAR/non-PAR boundary automatically.

See Ploidy & Special Chromosomes for exact PAR coordinates and genotype counting rules for haploid regions.

Next Steps