CFAP69 p.Leu369=
c.1107A>G · rs187154772 · VCV740372
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.337%, 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 2.1 | GERP 1.3, phastCons 1 |
| Overall | ||
| CADD | 3.705 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.337%
African / African-American · 249/73,902 alleles
Filtering AF
0.303%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.289%
Overall
0.0179%
285/1,591,910 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.337% | 297 |
| Admixed American | 0.0302% | 3,311 |
| Remaining individualsnot grpmax-eligible | 0.0195% | 5,133 |
| South Asian | 0.00114% | 87,474 |
| European (non-Finnish) | 0.000513% | 194,807 |
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.Leu369=
- Coding
- c.1107A>G
- MANE Select
- NM_001039706
- dbSNP
- rs187154772
- Type
- single nucleotide variant
- Location
- chr7:90277286 (GRCh38)
- Gene constraint
- LOEUF 1 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.48
- Residue 369
- a UniProt-annotated variant site (in spgf24)
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.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-leu369 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown