CFHR2 p.Lys38=
c.114A>G · rs143480813 · VCV2581640
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.224%, 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 -2.1 | GERP -3.3 |
| Overall | ||
| CADD | 0.464 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.224%
African / African-American · 168/75,042 alleles
Filtering AF
0.196%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.186%
Overall
0.0128%
206/1,613,946 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.224% | 447 |
| Admixed American | 0.03% | 3,331 |
| Remaining individualsnot grpmax-eligible | 0.0272% | 3,676 |
| European (non-Finnish) | 0.000254% | 393,303 |
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.Lys38=
- Coding
- c.114A>G
- MANE Select
- NM_005666
- dbSNP
- rs143480813
- Type
- single nucleotide variant
- Location
- chr1:196949510 (GRCh38)
- Gene constraint
- LOEUF 1.498 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.90 · 4 PDB
- Residue 38
- the sushi 1 domain; a disulfide bond
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-lys38 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown