NBN p.Val151=
c.453C>T · rs1176879721 · VCV530772
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, mid)
Conditions
2
Nijmegen breakage syndrome
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 1.7 | GERP -1, phastCons 1 |
| Overall | ||
| CADD | 7.563 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
Middle Eastern · 1/6,054 alleles
Overall
0.000186%
3/1,613,146 alleles · ultra-rare
exomes 3/1,460,914 · genomes 0/152,232 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0165% | 6,054 |
| East Asian | 0.00223% | 44,782 |
| European (non-Finnish) | 8.48e-05% | 1,179,354 |
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
- NBN
- Protein
- p.Val151=
- Coding
- c.453C>T
- MANE Select
- NM_002485
- dbSNP
- rs1176879721
- Type
- single nucleotide variant
- Location
- chr8:89980761 (GRCh38)
- Structure
- AlphaFold pLDDT 75.83 · 5 PDB
- Residue 151
- a β-strand
Similar variants
- NBN p.Val151Phe Uncertain significance ★★ ⚠ same residue
- NBN p.Val151Ile Uncertain significance ★ ⚠ same residue
- NBN p.Val151fs Pathogenic ★ same residue
- NBN c.1124+1G>C Likely pathogenic ★★ same condition
- NBN c.1124+2T>G Likely pathogenic ★★ same condition
- NBN c.1397+2T>A Likely pathogenic ★★ same condition
- NBN c.171+1G>A Likely pathogenic ★★ same condition
- NBN c.172-1G>T Likely pathogenic ★★ same condition
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/nbn-p-val151 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown