CHRNB2 p.Pro259=
c.777A>T · rs770431355 · VCV381738
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
very rare (popmax 0.000339%, 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 -6.5 | GERP -4 |
| Overall | ||
| CADD | 0.308 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000339%
European (non-Finnish) · 4/1,180,038 alleles
Filtering AF
7.9e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.4e-05%
Overall
0.000274%
4/1,461,882 alleles · very rare
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
- CHRNB2
- Protein
- p.Pro259=
- Coding
- c.777A>T
- MANE Select
- NM_000748
- dbSNP
- rs770431355
- Type
- single nucleotide variant
- Location
- chr1:154571600 (GRCh38)
- Gene constraint
- LOEUF 1.116 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.16 · 15 PDB
Similar variants
- CHRNB2 p.Val287Leu Pathogenic/Likely pathogenic ★★ same type
- CHRNB2 p.Val287Met Pathogenic ★★ same type
- CHRNB2 p.Val308Ala Pathogenic/Likely pathogenic ★★ same type
- CHRNB2 c.1338+3G>T Uncertain significance ★★ same type
- CHRNB2 c.366-3C>T Uncertain significance ★★ same type
- CHRNB2 p.Ala135Val Uncertain significance ★★ ⚠ same type
- CHRNB2 p.Ala154Thr Uncertain significance ★★ ⚠ same type
- CHRNB2 p.Ala207Gly 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/chrnb2-p-pro259 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown