CFAP69 p.Ala182=
c.546G>A · rs138300755 · VCV709810
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.1%, 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 -0.066 | GERP -9.4, phastCons 0.67 |
| Overall | ||
| CADD | 7.164 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.1%
African / African-American · 1,572/74,890 alleles
Filtering AF
2.01%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.98%
Overall
0.149%
2,395/1,611,198 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.1% | 48 |
| Middle Eastern | 0.584% | 171 |
| Admixed American | 0.351% | 285 |
| Remaining individualsnot grpmax-eligible | 0.266% | 375 |
| European (non-Finnish) | 0.0353% | 2,835 |
| Finnishnot grpmax-eligible | 0.00156% | 63,986 |
| South Asian | 0.0011% | 90,652 |
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.Ala182=
- Coding
- c.546G>A
- MANE Select
- NM_001039706
- dbSNP
- rs138300755
- Type
- single nucleotide variant
- Location
- chr7:90271539 (GRCh38)
- Gene constraint
- LOEUF 1 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.48
Similar variants
- CFAP69 p.Ala182Val Uncertain significance ★ ⚠ same residue
- 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.Ala8= Benign/Likely benign ★★ same type
- CFAP69 p.Arg106His 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-ala182 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown