RNF2 p.Asn8=
c.24C>T · rs201683390 · VCV2639639
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0267%, amr)
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 -2 | GERP -3.6 |
| Overall | ||
| CADD | 6.851 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0267%
Admixed American · 16/60,010 alleles
Filtering AF
0.0202%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0194%
Overall
0.0185%
298/1,614,036 alleles · ultra-rare
exomes 267/1,461,764 · genomes 31/152,272 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0267% | 3,751 |
| European (non-Finnish) | 0.0225% | 4,453 |
| Remaining individualsnot grpmax-eligible | 0.0176% | 5,682 |
| Middle Eastern | 0.0165% | 6,062 |
| African / African-American | 0.00533% | 18,760 |
| South Asian | 0.0011% | 91,074 |
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
- RNF2
- Protein
- p.Asn8=
- Coding
- c.24C>T
- MANE Select
- NM_007212
- dbSNP
- rs201683390
- Type
- single nucleotide variant
- Location
- chr1:185087577 (GRCh38)
- Gene constraint
- LOEUF 0.321 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 78.27 · 28 PDB
- Residue 8
- the 'interaction with hip2' region
Similar variants
- BAP1 p.Leu8Pro Uncertain significance ★★ ⚠ same residue
- RNF2 p.Asn8Tyr Uncertain significance ★★ ⚠ same residue
- BAP1 p.Leu8= Likely benign ★★ same residue
- BAP1 p.Leu8_Ser10delinsArg Uncertain significance ★ same residue
- BAP1 c.1117-1G>A Likely pathogenic ★★ same type
- BAP1 c.122+1G>A Pathogenic ★★ same type
- BAP1 c.122+1G>T Pathogenic/Likely pathogenic ★★ same type
- BAP1 c.122+5G>A 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/rnf2-p-asn8 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown