RRM2B p.Phe183=
c.549T>C · rs759840326 · VCV2895560
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00162%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.186 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 2.2 | GERP -0.82, phastCons 1 |
| Overall | ||
| CADD | 11.95 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00162%
European (non-Finnish) · 19/1,174,538 alleles
Filtering AF
0.00103%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000834%
Overall
0.00131%
21/1,608,050 alleles · very rare
exomes 21/1,455,702 · genomes 0/152,348 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00162% | 61,818 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,308 |
| Finnishnot grpmax-eligible | 0.00156% | 63,902 |
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
- RRM2B
- Protein
- p.Phe183=
- Coding
- c.549T>C
- MANE Select
- NM_015713
- dbSNP
- rs759840326
- Type
- single nucleotide variant
- Location
- chr8:102224047 (GRCh38)
- Gene constraint
- LOEUF 0.688 · pLI 0.27 (gnomAD)
- Structure
- AlphaFold pLDDT 85.73 · 3 PDB
- Residue 183
- an α-helix
Similar variants
- RRM2B c.322-2A>G Pathogenic ★★ same type
- RRM2B c.455+1G>A Likely pathogenic ★★ same type
- RRM2B p.Arg110Cys Likely pathogenic ★★ same type
- RRM2B p.Arg174Ter Pathogenic/Likely pathogenic ★★ same type
- RRM2B p.Arg327Ter Pathogenic ★★ same type
- RRM2B p.Arg41Trp Pathogenic/Likely pathogenic ★★ same type
- RRM2B p.Gly229Val Pathogenic/Likely pathogenic ★★ same type
- RRM2B p.Ile224Ser Pathogenic/Likely pathogenic ★★ 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/rrm2b-p-phe183 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown