NBEA p.Val949=
c.2847C>T · VCV3388078
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0683%, 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 0.89 | GERP 1.3, phastCons 1 |
| Overall | ||
| CADD | 12.38 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0683%
Middle Eastern · 4/5,858 alleles
Filtering AF
0.0233%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.014%
Overall
0.00425%
67/1,578,126 alleles · ultra-rare
exomes 63/1,426,212 · genomes 4/151,914 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0683% | 1,464 |
| Remaining individualsnot grpmax-eligible | 0.00493% | 20,287 |
| South Asian | 0.00473% | 21,142 |
| European (non-Finnish) | 0.00463% | 21,596 |
| Admixed American | 0.00384% | 26,070 |
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.Val949=
- Coding
- c.2847C>T
- MANE Select
- NM_001385012
- Type
- single nucleotide variant
- Location
- chr13:35159018 (GRCh38)
- Gene constraint
- LOEUF 0.137 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Residue 949
- 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-val949 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown