CFAP69 c.682+50A>C
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 100%, eas) — too common for a highly-penetrant pathogenic allele
Conditions
1
spermatogenic failure 24
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +50 | near-intronic (+50 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.7 | GERP -5.3 |
| Non-coding constraint | Z 1.65 | 1 kb window · o/e 0.87 · regional · uncalibrated |
| Overall | ||
| CADD | 0.473 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
100%
East Asian · 44,590/44,612 alleles
Filtering AF
99.2%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 98.9%
Overall
86.5%
1,374,305/1,588,948 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 100% | 1 |
| African / African-American | 97.3% | 1 |
| South Asian | 92.9% | 1 |
| Finnishnot grpmax-eligible | 90.5% | 1 |
| Admixed American | 89.8% | 1 |
| Middle Eastern | 89.4% | 1 |
| Remaining individualsnot grpmax-eligible | 87.5% | 1 |
| Amishnot grpmax-eligible | 85.5% | 1 |
| European (non-Finnish) | 84.4% | 1 |
| Ashkenazi Jewishnot grpmax-eligible | 83.9% | 1 |
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
- Coding
- c.682+50A>C
- MANE Select
- NM_001039706
- dbSNP
- rs10280053
- Type
- single nucleotide variant
- Location
- chr7:90271725 (GRCh38)
- Gene constraint
- LOEUF 1 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.48
Similar variants
- CFAP69 c.1857+47T>A Benign ★★ same condition
- CFAP69 p.Ser854Arg Benign ★★ same condition
- CFAP69 p.Thr885Met Benign ★★ ⚠ same condition
- CFAP69 p.Val490Met Benign ★★ same condition
- CFAP69 c.860+1G>A Pathogenic same condition
- CFAP69 p.Gln255Ter Pathogenic same condition
- CFAP69 p.Trp216Ter Pathogenic same condition
- CFAP69 p.Leu357fs Pathogenic same condition
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-c-682-plus-50a-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown