BEAN1 p.Cys220=
c.660C>T · rs779019822 · VCV3052744
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00198%, amr)
Conditions
1
BEAN1-related disorder
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 -0.001 | GERP -1.2, phastCons 0.97 |
| Overall | ||
| CADD | 6.302 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00198%
Admixed American · 1/50,568 alleles
Filtering AF
0.000371%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000268%
Overall
0.000712%
11/1,544,202 alleles · very rare
exomes 10/1,391,978 · genomes 1/152,224 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00198% | 50,568 |
| Remaining individualsnot grpmax-eligible | 0.00167% | 59,768 |
| European (non-Finnish) | 0.000788% | 126,981 |
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.Cys220=
- Coding
- c.660C>T
- MANE Select
- NM_001178020
- dbSNP
- rs779019822
- Type
- single nucleotide variant
- Location
- chr16:66480805 (GRCh38)
- Gene constraint
- LOEUF 1.45 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 58.44
- Residue 220
- the 'disordered' region
Disease context
BEAN1-related disorder
Similar variants
- BEAN1 c.289+10C>T Benign same condition
- BEAN1 c.*1G>C Likely benign same condition
- BEAN1 c.*97C>T Benign same condition
- 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
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-cys220 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown