BEAN1 p.Ser26=
c.78G>A · VCV4930373
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0167%, mid)
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 -6.3 | GERP -3 |
| Overall | ||
| CADD | 3.754 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0167%
Middle Eastern · 1/5,988 alleles
Filtering AF
0.00194%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00104%
Overall
0.00156%
24/1,535,956 alleles · ultra-rare
exomes 24/1,383,738 · genomes 0/152,218 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0167% | 5,988 |
| East Asian | 0.00733% | 13,635 |
| South Asian | 0.00238% | 42,023 |
| Admixed American | 0.00196% | 50,998 |
| Remaining individualsnot grpmax-eligible | 0.00167% | 60,028 |
| European (non-Finnish) | 0.0014% | 71,675 |
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.Ser26=
- Coding
- c.78G>A
- MANE Select
- NM_001178020
- Type
- single nucleotide variant
- Location
- chr16:66469654 (GRCh38)
- Gene constraint
- LOEUF 1.45 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 58.44
Similar variants
- BEAN1 p.Ser26Leu 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-ser26 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown