CFAP69 p.Ala12=
c.36C>T · rs17865323 · VCV768178
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 5.25%, afr) — too common for a highly-penetrant pathogenic allele
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 2.9 | GERP 3, phastCons 0.087 |
| Overall | ||
| CADD | 12.21 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
5.25%
African / African-American · 3,690/70,268 alleles
Filtering AF
5.11%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.05%
Overall
0.266%
4,134/1,556,230 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 5.25% | 19 |
| Remaining individualsnot grpmax-eligible | 0.368% | 272 |
| Admixed American | 0.314% | 319 |
| Middle Eastern | 0.241% | 416 |
| South Asian | 0.0176% | 5,688 |
| European (non-Finnish) | 0.00312% | 32,065 |
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.Ala12=
- Coding
- c.36C>T
- MANE Select
- NM_001039706
- dbSNP
- rs17865323
- Type
- single nucleotide variant
- Location
- chr7:90245460 (GRCh38)
- Gene constraint
- LOEUF 1 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.48
- Residue 12
- 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.Ala182= Benign ★★ same type
- CFAP69 p.Ala8= Benign/Likely 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-ala12 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown