Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Common
common (popmax 13.6%, afr) — too common for a highly-penetrant pathogenic allele
Conditions
1
primary ciliary dyskinesia
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.2 | GERP -0.19, phastCons 0.19 |
| Overall | ||
| CADD | 6.221 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
13.6%
African / African-American · 8,801/64,826 alleles
Filtering AF
13.3%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 13.2%
Overall
0.764%
9,852/1,289,962 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 13.6% | 7 |
| Admixed American | 1.05% | 95 |
| Remaining individualsnot grpmax-eligible | 0.944% | 106 |
| Middle Eastern | 0.676% | 148 |
| South Asian | 0.0516% | 1,939 |
| European (non-Finnish) | 0.0289% | 3,461 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- DNAAF5
- Protein
- p.Ala24=
- Coding
- c.72G>A
- MANE Select
- NM_017802
- dbSNP
- rs9719797
- Type
- single nucleotide variant
- Location
- chr7:726792 (GRCh38)
- Gene constraint
- LOEUF 1.12 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 92.80
Disease context
primary ciliary dyskinesia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Primary ciliary dyskinesia (Orphanet):
- Inheritance
- Autosomal dominant, Autosomal recessive, X-linked recessive
- Onset
- Neonatal
- Prevalence
- 1-5 / 10 000 (Pakistan)
Similar variants
- DNAAF5 c.1470+1G>A Likely pathogenic ★★ same condition
- DNAAF5 c.1615-2A>G Likely pathogenic ★★ same condition
- DNAAF5 p.Arg253Ter Pathogenic/Likely pathogenic ★★ same condition
- DNAAF5 p.Cys500Phe Pathogenic/Likely pathogenic ★★ ⚠ same condition
- DNAAF5 p.Leu795Pro Pathogenic/Likely pathogenic ★★ same condition
- DNAAF5 p.Trp309Ter Pathogenic/Likely pathogenic ★★ same condition
- DNAAF5 c.780+6T>A Uncertain significance ★★ same condition
- DNAAF5 c.905+4C>T Uncertain significance ★★ same condition
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/dnaaf5-p-ala24 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown