CFAP44 p.Leu893=
c.2679A>G · rs35480872 · VCV716190
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
rare (popmax 0.238%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.058 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP -0.86 | GERP -0.5 |
| Overall | ||
| CADD | 2.821 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.238%
Admixed American · 143/60,008 alleles
Filtering AF
0.225%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.222%
Overall
0.192%
3,099/1,613,748 alleles · rare
exomes 2,870/1,461,452 · genomes 229/152,296 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.238% | 420 |
| European (non-Finnish) | 0.233% | 430 |
| Remaining individualsnot grpmax-eligible | 0.202% | 496 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0608% | 1,644 |
| Finnishnot grpmax-eligible | 0.05% | 2,001 |
| African / African-American | 0.044% | 2,274 |
| Middle Eastern | 0.0165% | 6,058 |
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
- CFAP44
- Protein
- p.Leu893=
- Coding
- c.2679A>G
- MANE Select
- NM_001164496
- dbSNP
- rs35480872
- Type
- single nucleotide variant
- Location
- chr3:113366075 (GRCh38)
- Gene constraint
- LOEUF 0.697 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 74.87 · 1 PDB
- Residue 893
- a UniProt-annotated variant site (in spgf20)
Similar variants
- CFAP44 p.Glu463Ter Pathogenic ★★ same type
- CFAP44 c.4759-3C>T Benign ★★ same type
- CFAP44 p.Ala157= Benign ★★ same type
- CFAP44 p.Ala486Val Likely benign ★★ same type
- CFAP44 p.Arg1059Gln Benign ★★ same type
- CFAP44 p.Arg1495Trp Benign ★★ ⚠ same type
- CFAP44 p.Arg1651Trp Benign/Likely benign ★★ same type
- CFAP44 p.Arg1806= Benign/Likely 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/cfap44-p-leu893 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown