CACNB2 p.Asn28=
c.84C>T · rs763573123 · VCV384804
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00144%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>G here scores Δ0.26 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.6 | GERP 0.83, phastCons 1 |
| Overall | ||
| CADD | 14.69 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00144%
European (non-Finnish) · 17/1,176,954 alleles
Filtering AF
0.00088%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000719%
Overall
0.00112%
18/1,604,210 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00144% | 69,232 |
| South Asian | 0.00112% | 89,418 |
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
- CACNB2
- Protein
- p.Asn28=
- Coding
- c.84C>T
- MANE Select
- NM_201596
- dbSNP
- rs763573123
- Type
- single nucleotide variant
- Location
- chr10:18140820 (GRCh38)
- Gene constraint
- LOEUF 0.77 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 65.78 · 3 PDB
Similar variants
- CACNB2 c.1206+5G>A Uncertain significance ★★ same type
- CACNB2 c.1303-3C>T Uncertain significance ★★ same type
- CACNB2 c.1488+6G>A Uncertain significance ★★ same type
- CACNB2 p.Ala105Thr Uncertain significance ★★ ⚠ same type
- CACNB2 p.Ala118Val Uncertain significance ★★ ⚠ same type
- CACNB2 p.Ala128Val Uncertain significance ★★ ⚠ same type
- CACNB2 p.Ala139Ser Uncertain significance ★★ ⚠ same type
- CACNB2 p.Ala229Asp 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/cacnb2-p-asn28 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown