NBEA p.Val2137=
c.6411C>T · VCV4919823
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000512%, nfe)
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 0.64 | GERP 0.78, phastCons 1 |
| Overall | ||
| CADD | 6.127 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000512%
European (non-Finnish) · 6/1,170,790 alleles
Filtering AF
0.000184%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000121%
Overall
0.000376%
6/1,597,448 alleles · very rare
exomes 6/1,445,186 · genomes 0/152,262 · joint denominator
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
- NBEA
- Protein
- p.Val2137=
- Coding
- c.6411C>T
- MANE Select
- NM_001385012
- Type
- single nucleotide variant
- Location
- chr13:35452198 (GRCh38)
- Gene constraint
- LOEUF 0.137 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Residue 2137
- a UniProt-annotated variant site (in nedege)
Similar variants
- NBEA p.Arg1299Ter Pathogenic/Likely pathogenic ★★ same type
- NBEA p.Arg145Ter Pathogenic/Likely pathogenic ★★ same type
- NBEA p.Arg2213Ter Pathogenic/Likely pathogenic ★★ same type
- NBEA p.Arg2866Ter Pathogenic ★★ same type
- NBEA p.Arg696Ter Pathogenic/Likely pathogenic ★★ same type
- NBEA p.Asp319Tyr Likely pathogenic ★★ same type
- NBEA c.4242+5G>A Uncertain significance ★★ same type
- NBEA p.Ala603Val 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/nbea-p-val2137 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown