CFAP69 p.Ile562=
c.1686C>T · rs188534119 · VCV712005
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.76%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>A here scores Δ0.47 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.7 | GERP 0.44, phastCons 0.39 |
| Overall | ||
| CADD | 4.742 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.76%
African / African-American · 2,065/74,888 alleles
Filtering AF
2.66%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.62%
Overall
0.147%
2,360/1,610,472 alleles · low-frequency
exomes 1,133/1,458,368 · genomes 1,227/152,104 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.76% | 36 |
| Admixed American | 0.2% | 500 |
| Remaining individualsnot grpmax-eligible | 0.194% | 515 |
| Middle Eastern | 0.0828% | 1,207 |
| European (non-Finnish) | 0.00382% | 26,165 |
| South Asian | 0.0033% | 30,261 |
| Finnishnot grpmax-eligible | 0.00156% | 63,912 |
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.Ile562=
- Coding
- c.1686C>T
- MANE Select
- NM_001039706
- dbSNP
- rs188534119
- Type
- single nucleotide variant
- Location
- chr7:90288263 (GRCh38)
- Gene constraint
- LOEUF 1 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.48
- Residue 562
- 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-ile562 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown