CFAP43 p.Leu802=
c.2406G>A · rs140481816 · VCV791031
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.95%, 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 0.36 | GERP -1.3, phastCons 0.022 |
| Overall | ||
| CADD | 6.841 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.95%
African / African-American · 1,464/74,888 alleles
Filtering AF
1.87%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.84%
Overall
0.123%
1,990/1,612,942 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.95% | 51 |
| Middle Eastern | 0.314% | 319 |
| Admixed American | 0.294% | 341 |
| Remaining individualsnot grpmax-eligible | 0.205% | 488 |
| Ashkenazi Jewishnot grpmax-eligible | 0.2% | 501 |
| European (non-Finnish) | 0.0119% | 8,425 |
| South Asian | 0.0044% | 22,749 |
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.Leu802=
- Coding
- c.2406G>A
- MANE Select
- NM_025145
- dbSNP
- rs140481816
- Type
- single nucleotide variant
- Location
- chr10:104179083 (GRCh38)
- Gene constraint
- LOEUF 0.78 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.27 · 1 PDB
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.Pro246= Benign ★★ same type
- CFAP43 p.Ser296= 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-leu802 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown