Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.17%, 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 0.81 | GERP -0.24, phastCons 0.57 |
| Overall | ||
| CADD | 2.453 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.17%
African / African-American · 1,627/75,032 alleles
Filtering AF
2.08%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.05%
Overall
0.177%
2,863/1,614,070 alleles · low-frequency
exomes 1,831/1,461,794 · genomes 1,032/152,276 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.17% | 46 |
| Middle Eastern | 0.775% | 129 |
| Admixed American | 0.468% | 214 |
| Remaining individualsnot grpmax-eligible | 0.322% | 311 |
| European (non-Finnish) | 0.0582% | 1,718 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0236% | 4,229 |
| South Asian | 0.0132% | 7,589 |
| East Asian | 0.00223% | 44,882 |
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
- RFC2
- Protein
- p.Arg201=
- Coding
- c.601A>C
- MANE Select
- NM_181471
- dbSNP
- rs1805392
- Type
- single nucleotide variant
- Location
- chr7:74240030 (GRCh38)
- Gene constraint
- LOEUF 1.394 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.63 · 16 PDB
- Residue 201
- an α-helix
Similar variants
- RFC2 p.Ala196Thr Uncertain significance ★★ ⚠ same type
- RFC2 c.759+8C>T Benign ★★ same type
- RFC2 p.Ala232Val Likely benign ★★ same type
- RFC2 p.His33= Benign ★★ same type
- RFC2 p.Thr129= Benign ★★ same type
- RFC2 p.Ala150Val Uncertain significance ★ ⚠ same type
- RFC2 p.Ala15Val Uncertain significance ★ ⚠ same type
- RFC2 p.Arg189Trp Uncertain significance ★ ⚠ 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/rfc2-p-arg201 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown