RFC2 p.Thr129=
c.387T>A · rs111490006 · VCV722291
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.04%, 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 -0.61 | GERP -1 |
| Overall | ||
| CADD | 5.662 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.04%
African / African-American · 1,529/75,004 alleles
Filtering AF
1.95%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.92%
Overall
0.105%
1,699/1,613,374 alleles · low-frequency
exomes 830/1,461,072 · genomes 869/152,302 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.04% | 49 |
| Remaining individualsnot grpmax-eligible | 0.131% | 762 |
| Admixed American | 0.107% | 936 |
| Middle Eastern | 0.066% | 1,514 |
| South Asian | 0.0033% | 30,335 |
| European (non-Finnish) | 0.00144% | 69,387 |
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.Thr129=
- Coding
- c.387T>A
- MANE Select
- NM_181471
- dbSNP
- rs111490006
- Type
- single nucleotide variant
- Location
- chr7:74246709 (GRCh38)
- Gene constraint
- LOEUF 1.394 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.63 · 16 PDB
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.Arg201= Benign ★★ same type
- RFC2 p.His33= 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-thr129 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown