CFHR2 p.Asn180=
c.540C>T · VCV3629855
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.124%, 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 -14 | GERP -2 |
| Overall | ||
| CADD | 0.593 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.124%
African / African-American · 93/75,008 alleles
Filtering AF
0.104%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.096%
Overall
0.00657%
106/1,613,736 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.124% | 807 |
| Remaining individualsnot grpmax-eligible | 0.0112% | 8,926 |
| Admixed American | 0.00667% | 14,997 |
| European (non-Finnish) | 0.00017% | 589,877 |
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
- CFHR2
- Protein
- p.Asn180=
- Coding
- c.540C>T
- MANE Select
- NM_005666
- Type
- single nucleotide variant
- Location
- chr1:196958000 (GRCh38)
- Gene constraint
- LOEUF 1.498 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.90 · 4 PDB
- Residue 180
- a disulfide bond; the sushi 3 domain
Similar variants
- CFHR2 p.Val16Ala Uncertain significance ★★ ⚠ same type
- CFHR2 c.430+141T>A Benign ★★ same type
- CFHR2 c.430+20C>T Benign ★★ same type
- CFHR2 c.430+7G>A Benign/Likely benign ★★ same type
- CFHR2 c.431-48C>A Benign ★★ same type
- CFHR2 c.431-65C>T Benign ★★ same type
- CFHR2 c.58+129C>G Benign ★★ same type
- CFHR2 c.-65C>G 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/cfhr2-p-asn180 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown