CFAP46 p.Pro203=
c.609G>A · rs754603805 · VCV2640997
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.066%, 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 -20 | GERP -4.8 |
| Overall | ||
| CADD | 0.126 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.066%
Middle Eastern · 4/6,062 alleles
Filtering AF
0.0225%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0135%
Overall
0.00583%
94/1,613,610 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.066% | 1,516 |
| Admixed American | 0.00833% | 12,001 |
| South Asian | 0.00769% | 13,009 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,623 |
| European (non-Finnish) | 0.00619% | 16,164 |
| East Asian | 0.00223% | 44,870 |
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
- CFAP46
- Protein
- p.Pro203=
- Coding
- c.609G>A
- MANE Select
- NM_001200049
- dbSNP
- rs754603805
- Type
- single nucleotide variant
- Location
- chr10:132937603 (GRCh38)
- Gene constraint
- LOEUF 0.888 · pLI <0.01 (gnomAD)
Similar variants
- CFAP46 p.Ala1708Val Uncertain significance ★ ⚠ same type
- CFAP46 p.Ala1742Glu Uncertain significance ★ ⚠ same type
- CFAP46 p.Ala1742Val Uncertain significance ★ ⚠ same type
- CFAP46 p.Ala1746Glu Uncertain significance ★ ⚠ same type
- CFAP46 p.Ala1788Val Uncertain significance ★ ⚠ same type
- CFAP46 p.Ala1806Val Uncertain significance ★ ⚠ same type
- CFAP46 p.Ala1811Val Uncertain significance ★ ⚠ same type
- CFAP46 p.Ala1871Val 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/cfap46-p-pro203 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown