CFHR3 p.Leu9=
c.27G>A · rs1359238447 · VCV709013
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0331%, 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 |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -3.7 | GERP -3.2 |
| Overall | ||
| CADD | 1.086 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0331%
Admixed American · 19/57,438 alleles
Filtering AF
0.0216%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.018%
Overall
0.0154%
21/136,672 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0331% | 3,023 |
| East Asian | 0.00224% | 44,562 |
| African / African-American | 0.00165% | 60,724 |
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.Leu9=
- Coding
- c.27G>A
- MANE Select
- NM_021023
- dbSNP
- rs1359238447
- Type
- single nucleotide variant
- Location
- chr1:196774913 (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-leu9 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown