CFAP46 p.Thr1697=
c.5091G>A · rs78376398 · VCV2640982
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0176%, amr)
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 |
|---|---|---|
| Pangolin | Δ0.21 | loss · gain 0.04 · not in the SpliceAI release · independent |
| Constraint at this position | ||
| Conservation | phyloP 0.49 | GERP -1.5, phastCons 0.098 |
| Overall | ||
| CADD | 15.87 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0176%
Admixed American · 9/50,994 alleles
Filtering AF
0.00917%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00678%
Overall
0.004%
62/1,550,620 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0176% | 5,666 |
| Remaining individualsnot grpmax-eligible | 0.0116% | 8,595 |
| South Asian | 0.00833% | 12,007 |
| East Asian | 0.00489% | 20,465 |
| European (non-Finnish) | 0.00323% | 31,000 |
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.Thr1697=
- Coding
- c.5091G>A
- MANE Select
- NM_001200049
- dbSNP
- rs78376398
- Type
- single nucleotide variant
- Location
- chr10:132860782 (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-thr1697 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown