CFAP52 p.Ile79=
c.237C>T · rs199772187 · VCV772779
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.215%, mid)
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 -4 | GERP -3.8 |
| Overall | ||
| CADD | 1.751 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.215%
Middle Eastern · 13/6,056 alleles
Filtering AF
0.127%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.101%
Overall
0.00372%
60/1,613,716 alleles · rare
exomes 52/1,461,724 · genomes 8/151,992 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.215% | 466 |
| Admixed American | 0.0384% | 2,607 |
| African / African-American | 0.00667% | 14,986 |
| East Asian | 0.00223% | 44,826 |
| South Asian | 0.0022% | 45,536 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,494 |
| European (non-Finnish) | 0.00127% | 78,659 |
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
- CFAP52
- Protein
- p.Ile79=
- Coding
- c.237C>T
- MANE Select
- NM_145054
- dbSNP
- rs199772187
- Type
- single nucleotide variant
- Location
- chr17:9585939 (GRCh38)
- Gene constraint
- LOEUF 1.022 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 93.59 · 2 PDB
Similar variants
- CFAP52 p.Ile79Phe Uncertain significance ★ ⚠ same residue
- CFAP52 p.Ala147Thr Uncertain significance ★★ ⚠ same type
- CFAP52 p.Ala161Asp Uncertain significance ★★ ⚠ same type
- CFAP52 p.Arg106Gln Uncertain significance ★★ ⚠ same type
- CFAP52 p.Arg170Gln Uncertain significance ★★ ⚠ same type
- CFAP52 p.Arg594Cys Uncertain significance ★★ ⚠ same type
- CFAP52 p.Gly343Ser Uncertain significance ★★ ⚠ same type
- CFAP52 p.Gly534Ala 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/cfap52-p-ile79 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown