BEAN1 p.Asp164=
c.492C>T · VCV4930382
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00683%, afr)
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 -8.2 | GERP -3 |
| Overall | ||
| CADD | 0.388 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00683%
African / African-American · 5/73,154 alleles
Filtering AF
0.0026%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00165%
Overall
0.00123%
19/1,550,956 alleles · very rare
exomes 15/1,398,664 · genomes 4/152,292 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00683% | 14,631 |
| Admixed American | 0.00392% | 25,483 |
| East Asian | 0.00244% | 40,906 |
| South Asian | 0.00238% | 42,004 |
| Finnishnot grpmax-eligible | 0.00167% | 59,888 |
| European (non-Finnish) | 0.000698% | 143,308 |
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.Asp164=
- Coding
- c.492C>T
- MANE Select
- NM_001178020
- Type
- single nucleotide variant
- Location
- chr16:66480637 (GRCh38)
- Gene constraint
- LOEUF 1.45 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 58.44
- Residue 164
- the 'disordered' region
Similar variants
- BEAN1 p.Asp164Gly Uncertain significance ★ ⚠ same residue
- 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.Pro167= Likely benign ★★ same type
- BEAN1 p.Tyr216= Likely benign ★★ same type
- BEAN1 p.Tyr96= Likely benign ★★ 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-asp164 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown