NBN p.Val101=
c.303G>A · rs1554568287 · VCV2035282
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00133%, afr)
Conditions
1
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 -1.5 | GERP -3.4 |
| Overall | ||
| CADD | 4.394 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00133%
African / African-American · 1/75,020 alleles
Overall
6.2e-05%
1/1,614,022 alleles · very rare
exomes 1/1,461,726 · genomes 0/152,296 · 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
- NBN
- Protein
- p.Val101=
- Coding
- c.303G>A
- MANE Select
- NM_002485
- dbSNP
- rs1554568287
- Type
- single nucleotide variant
- Location
- chr8:89981392 (GRCh38)
- Structure
- AlphaFold pLDDT 75.83 · 5 PDB
- Residue 101
- the 'disordered' region
Similar variants
- NBN p.Val101Ala Uncertain significance ★★ same residue
- NBN p.Val101Gly Uncertain significance ★★ ⚠ same residue
- NBN p.Val101Met Uncertain significance ★★ 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-val101 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown