NBEAL2 p.Ala487=
c.1461C>A · VCV3895967
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 1,558,980)
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 2.1 | GERP 1.6, phastCons 1 |
| Overall | ||
| CADD | 10.8 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,558,980). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- NBEAL2
- Protein
- p.Ala487=
- Coding
- c.1461C>A
- MANE Select
- NM_015175
- Type
- single nucleotide variant
- Location
- chr3:46995196 (GRCh38)
- Gene constraint
- LOEUF 0.641 · pLI <0.01 (gnomAD)
Similar variants
- NBEAL2 c.4485-1G>A Pathogenic/Likely pathogenic ★★ same type
- NBEAL2 c.4485-1G>T Pathogenic/Likely pathogenic ★★ same type
- NBEAL2 p.Arg2120Gln Likely pathogenic ★★ same type
- NBEAL2 p.Arg597Ter Pathogenic ★★ same type
- NBEAL2 p.Glu1361Ter Pathogenic ★★ same type
- NBEAL2 c.2557-5C>G Uncertain significance ★★ same type
- NBEAL2 c.5459+8G>A Uncertain significance ★★ same type
- NBEAL2 c.*267G>C 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/nbeal2-p-ala487 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown