RAD50 p.Val101=
c.303G>A · rs781766028 · VCV457432
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00128%, nfe)
Conditions
1
hereditary neoplastic syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.67 | donor gain · deltas |
|---|---|---|
| Pangolin | Δ0.68 | gain · loss 0.00 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 3.2 | GERP 2, phastCons 1 |
| Overall | ||
| CADD | 18.52 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00128%
European (non-Finnish) · 15/1,175,310 alleles
Filtering AF
0.000766%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000608%
Overall
0.000932%
15/1,608,938 alleles · very rare
exomes 15/1,456,630 · genomes 0/152,308 · 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
- RAD50
- Protein
- p.Val101=
- Coding
- c.303G>A
- MANE Select
- NM_005732
- dbSNP
- rs781766028
- Type
- single nucleotide variant
- Location
- chr5:132575866 (GRCh38)
- Gene constraint
- LOEUF 0.889 · pLI <0.01 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 82.83 · 6 PDB
Similar variants
- RAD50 p.Val101Ala Uncertain significance ★★ ⚠ same residue
- RAD50 p.Val101dup Uncertain significance ★ same residue
- RAD50 c.1051+1G>A Likely pathogenic ★★ same condition
- RAD50 c.1052-1G>A Likely pathogenic ★★ same condition
- RAD50 c.1052-1G>T Pathogenic/Likely pathogenic ★★ same condition
- RAD50 c.1052-2A>C Likely pathogenic ★★ same condition
- RAD50 c.1245+1G>A Pathogenic/Likely pathogenic ★★ same condition
- RAD50 c.129+1G>A 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/rad50-p-val101 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown