RFC2 p.Glu2=
c.6G>A · rs782510398 · VCV728257
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00555%, nfe)
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 0.56 | GERP 2.7, phastCons 0.12 |
| Overall | ||
| CADD | 7.905 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00555%
European (non-Finnish) · 65/1,170,360 alleles
Filtering AF
0.00447%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00407%
Overall
0.00419%
67/1,597,532 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00555% | 18,006 |
| Finnishnot grpmax-eligible | 0.00321% | 31,139 |
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.Glu2=
- Coding
- c.6G>A
- MANE Select
- NM_181471
- dbSNP
- rs782510398
- Type
- single nucleotide variant
- Location
- chr7:74254378 (GRCh38)
- Gene constraint
- LOEUF 1.394 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.63 · 16 PDB
- Residue 2
- the 'disordered' region
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.Thr129= Benign ★★ same type
- RFC2 p.Ala150Val Uncertain significance ★ ⚠ same type
- RFC2 p.Ala15Val 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-glu2 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown