CFHR3 p.Leu4=
c.10C>T · rs60627815 · VCV775632
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.13%, afr)
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 |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -2.9 | GERP -3.2 |
| Overall | ||
| CADD | 3.723 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.13%
African / African-American · 2,512/60,756 alleles
Filtering AF
4%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.95%
Overall
0.197%
3,018/1,528,294 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.13% | 24 |
| Middle Eastern | 0.541% | 185 |
| Remaining individualsnot grpmax-eligible | 0.281% | 356 |
| Admixed American | 0.251% | 398 |
| European (non-Finnish) | 0.0141% | 7,103 |
| South Asian | 0.00869% | 11,512 |
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
- CFHR3
- Protein
- p.Leu4=
- Coding
- c.10C>T
- MANE Select
- NM_021023
- dbSNP
- rs60627815
- Type
- single nucleotide variant
- Location
- chr1:196774896 (GRCh38)
- Gene constraint
- LOEUF 1.302 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 91.93
Similar variants
- CFHR3 c.796+1G>A Uncertain significance ★★ same type
- CFHR3 p.Arg320Gln Uncertain significance ★★ ⚠ same type
- CFHR3 p.Gly119Ala Uncertain significance ★★ ⚠ same type
- CFHR3 p.Ile70Thr Uncertain significance ★★ ⚠ same type
- CFHR3 p.Tyr118Ter Uncertain significance ★★ same type
- CFHR3 c.431-88C>T Benign ★★ same type
- CFHR3 c.58+8A>G Likely benign ★★ same type
- CFHR3 c.796+22T>A 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/cfhr3-p-leu4 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown