CFAP43 p.Ala1030=
c.3090A>G · rs146641264 · VCV1176268
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.016%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.021 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -2.2 | GERP -3.2 |
| Overall | ||
| CADD | 2.044 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.016%
African / African-American · 12/74,932 alleles
Filtering AF
0.00921%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00722%
Overall
0.000992%
16/1,613,050 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.016% | 6,244 |
| Admixed American | 0.00334% | 29,955 |
| European (non-Finnish) | 0.00017% | 589,723 |
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
- CFAP43
- Protein
- p.Ala1030=
- Coding
- c.3090A>G
- MANE Select
- NM_025145
- dbSNP
- rs146641264
- Type
- single nucleotide variant
- Location
- chr10:104164250 (GRCh38)
- Gene constraint
- LOEUF 0.78 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.27 · 1 PDB
- Residue 1030
- a UniProt-annotated variant site (in spgf19)
Similar variants
- CFAP43 p.Arg894Ter Pathogenic/Likely pathogenic ★★ same type
- CFAP43 p.Thr1075Lys Uncertain significance ★★ ⚠ same type
- CFAP43 c.2142-4A>G Benign ★★ same type
- CFAP43 p.Glu1540Gly Benign/Likely benign ★★ same type
- CFAP43 p.Leu1542Val Benign/Likely benign ★★ same type
- CFAP43 p.Leu616Phe Benign ★★ ⚠ same type
- CFAP43 p.Leu802= Benign ★★ same type
- CFAP43 p.Pro246= Benign ★★ 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/cfap43-p-ala1030 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown