CFAP69 p.Asn372=
c.1116C>T · rs3761805 · VCV3060732
Benign
No assertion criteria
Classification
Benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 68.6%, eas) — too common for a highly-penetrant pathogenic allele
Conditions
1
CFAP69-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.20 | donor loss · deltas |
|---|---|---|
| Pangolin | Δ0.27 | loss · gain 0.03 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 0.44 | GERP -2.7, phastCons 0.99 |
| Overall | ||
| CADD | 6.023 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
68.6%
East Asian · 30,225/44,066 alleles
Filtering AF
67.9%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 67.7%
Overall
22.1%
348,482/1,580,284 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 68.6% | 1 |
| Admixed American | 38.4% | 3 |
| African / African-American | 36.6% | 3 |
| South Asian | 28.7% | 3 |
| Ashkenazi Jewishnot grpmax-eligible | 26.3% | 4 |
| Middle Eastern | 25.9% | 4 |
| Remaining individualsnot grpmax-eligible | 24.9% | 4 |
| Finnishnot grpmax-eligible | 23.4% | 4 |
| Amishnot grpmax-eligible | 22.8% | 4 |
| European (non-Finnish) | 17.8% | 6 |
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.Asn372=
- Coding
- c.1116C>T
- MANE Select
- NM_001039706
- dbSNP
- rs3761805
- Type
- single nucleotide variant
- Location
- chr7:90277295 (GRCh38)
- Gene constraint
- LOEUF 1 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.48
- Residue 372
- a UniProt-annotated variant site (in spgf24)
Disease context
CFAP69-related disorder
Similar variants
- CFAP69 c.-7A>C Likely benign same condition
- CFAP69 p.Leu541= Likely benign same condition
- CFAP69 p.Met46Val Likely benign same condition
- CFAP69 p.Thr825Met Likely benign same condition
- CFAP69 p.Val894Gly Likely benign same condition
- CFAP69 p.Ile114fs Likely pathogenic ★ same condition
- CFAP69 p.Phe731Leu Uncertain significance ★★ ⚠ same type
- CFAP69 p.Tyr819His Uncertain significance ★★ ⚠ 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-asn372 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown