CFAP46 p.His1463=
c.4389C>T · rs950640282 · VCV2640985
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0997%, mid)
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 · G>C here scores Δ0.26 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.002 | GERP -4.6 |
| Overall | ||
| CADD | 2.624 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0997%
Middle Eastern · 6/6,018 alleles
Filtering AF
0.0434%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0296%
Overall
0.00613%
95/1,550,984 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0997% | 1,003 |
| European (non-Finnish) | 0.00724% | 13,821 |
| Admixed American | 0.00588% | 16,999 |
| Remaining individualsnot grpmax-eligible | 0.00332% | 30,112 |
| South Asian | 0.00119% | 84,066 |
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.His1463=
- Coding
- c.4389C>T
- MANE Select
- NM_001200049
- dbSNP
- rs950640282
- Type
- single nucleotide variant
- Location
- chr10:132872798 (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-his1463 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown