BEAN1 p.Pro167=
c.501A>G · rs141546513 · VCV2672642
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.176%, nfe)
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 -9.3 | GERP -3 |
| Overall | ||
| CADD | 0.265 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.176%
European (non-Finnish) · 2,016/1,146,836 alleles
Filtering AF
0.169%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.167%
Overall
0.14%
2,168/1,551,428 alleles · rare
exomes 2,037/1,399,210 · genomes 131/152,218 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.176% | 569 |
| Remaining individualsnot grpmax-eligible | 0.0965% | 1,036 |
| Admixed American | 0.0745% | 1,342 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0349% | 2,863 |
| African / African-American | 0.0301% | 3,324 |
| Finnishnot grpmax-eligible | 0.0267% | 3,743 |
| Middle Eastern | 0.0167% | 5,986 |
| South Asian | 0.00833% | 12,006 |
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
- BEAN1
- Protein
- p.Pro167=
- Coding
- c.501A>G
- MANE Select
- NM_001178020
- dbSNP
- rs141546513
- Type
- single nucleotide variant
- Location
- chr16:66480646 (GRCh38)
- Gene constraint
- LOEUF 1.45 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 58.44
- Residue 167
- the 'disordered' region
Similar variants
- BEAN1 p.Ala156Ser Uncertain significance ★★ ⚠ same type
- BEAN1 p.Arg90Gln Uncertain significance ★★ ⚠ same type
- BEAN1 p.Arg108His Likely benign ★★ same type
- BEAN1 p.Arg76Ser Benign/Likely benign ★★ same type
- BEAN1 p.Tyr216= Likely benign ★★ same type
- BEAN1 p.Tyr96= Likely benign ★★ same type
- BEAN1 p.Ala10Thr Uncertain significance ★ ⚠ same type
- BEAN1 p.Ala165Thr 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/bean1-p-pro167 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown