CFAP69 p.Ala8=
c.24G>T · rs149099697 · VCV709809
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.12%, afr)
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 -3.3 | GERP -7.7 |
| Overall | ||
| CADD | 1.236 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.12%
African / African-American · 1,495/70,586 alleles
Filtering AF
2.03%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.99%
Overall
0.145%
2,263/1,557,814 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.12% | 47 |
| Middle Eastern | 0.483% | 207 |
| Admixed American | 0.34% | 294 |
| Remaining individualsnot grpmax-eligible | 0.271% | 370 |
| European (non-Finnish) | 0.0347% | 2,879 |
| Finnishnot grpmax-eligible | 0.00158% | 63,210 |
| South Asian | 0.00117% | 85,664 |
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
- CFAP69
- Protein
- p.Ala8=
- Coding
- c.24G>T
- MANE Select
- NM_001039706
- dbSNP
- rs149099697
- Type
- single nucleotide variant
- Location
- chr7:90245448 (GRCh38)
- Gene constraint
- LOEUF 1 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.48
- Residue 8
- the 'disordered' region
Similar variants
- CFAP69 p.Phe731Leu Uncertain significance ★★ ⚠ same type
- CFAP69 p.Tyr819His Uncertain significance ★★ same type
- CFAP69 c.1857+47T>A Benign ★★ same type
- CFAP69 c.682+50A>C Benign ★★ same type
- CFAP69 p.Ala12= Benign ★★ same type
- CFAP69 p.Ala182= Benign ★★ same type
- CFAP69 p.Arg106His Benign ★★ same type
- CFAP69 p.Arg306Cys Benign ★★ same type
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/cfap69-p-ala8 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown