RFC2 p.Asp148=
c.444C>T · rs781826115 · VCV739219
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0245%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -8.9 | GERP -5.2 |
| Overall | ||
| CADD | 0.45 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0245%
East Asian · 11/44,858 alleles
Filtering AF
0.0137%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0106%
Overall
0.00186%
30/1,612,180 alleles · ultra-rare
exomes 26/1,460,082 · genomes 4/152,098 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0245% | 4,078 |
| Remaining individualsnot grpmax-eligible | 0.00481% | 20,807 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,580 |
| South Asian | 0.0033% | 30,335 |
| European (non-Finnish) | 0.00102% | 98,216 |
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.Asp148=
- Coding
- c.444C>T
- MANE Select
- NM_181471
- dbSNP
- rs781826115
- Type
- single nucleotide variant
- Location
- chr7:74243237 (GRCh38)
- Gene constraint
- LOEUF 1.394 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.63 · 16 PDB
- Residue 148
- 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.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-asp148 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown