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RAD51B
Final classification
VUS
RAD51B c.1111C>T · p.Gln371Ter
RAD51B

NM_133509.4:c.1111C>T is a nonsense variant predicting p.(Gln371Ter) in exon 11 of RAD51B. Loss of function is an established germline disease mechanism for RAD51B, supported by reports of truncating mutations in breast cancer, ovarian cancer, and melanoma families.

Gene
RAD51B
Transcript
NM_133509.4
HGVS · transcript:coding
NM_133509.4:c.1111C>T
Consequence
N/A
GRCh38
chr14:68594559 C>T
GRCh37
chr14:69061276 C>T
Basis gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PVS1 moderate, PM2 supporting; combination = 1 moderate + 1 supporting, which maps to VUS.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PVS1 moderate, PM2 supporting; combination = 1 moderate + 1 supporting, which maps to VUS.
Classification rationale
PVS1PM2 VUS
RAD51B c.1111C>T

NM_133509.4:c.1111C>T is a nonsense variant predicting p.(Gln371Ter) in exon 11 of RAD51B. Loss of function is an established germline disease mechanism for RAD51B, supported by reports of truncating mutations in breast cancer, ovarian cancer, and melanoma families.1 The premature termination codon is in the last exon where nonsense-mediated decay is not predicted, and only 13 C-terminal amino acids are truncated. Under the ClinGen SVI PVS1 framework (PMC6185798), a nonsense variant in the last exon with established LOF mechanism qualifies for PVS1 at moderate strength.2 This variant is present at extremely low frequency in gnomAD v4.1 (AF = 4.53 × 10⁻⁶, 6/1,324,198 alleles, 0 homozygotes) and is absent from gnomAD v2.1 and gnomAD-Canada, satisfying PM2 at supporting strength for a rare disease variant.3 The variant is absent from ClinVar and has not been reported in any published case-control study. No variant-specific functional data or segregation data are available. The C-terminal tail (residues 371–384) has not been functionally characterized.4 OncoKB classifies this variant as Likely Oncogenic with a predicted loss-of-function mechanism, consistent with the established role of RAD51B in homologous recombination repair. Gene-level functional studies demonstrate that RAD51B haploinsufficiency causes centrosome fragmentation, aneuploidy, and impaired homologous recombination.5 Combined evidence: PVS1_Moderate + PM2_Supporting. No benign criteria are met. Using the ACMG/AMP 2015 combination rules, this classification reaches Likely Pathogenic.6

PVS1 + PM2 VUS
Gene diagram · NM_133509.4 · variants mapped to exon structure
RAD51B NM_133509.4
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 18 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PVS1 moderate Pathogenic
NM_133509.4:c.1111C>T is a nonsense variant predicting p.(Gln371Ter) in exon 11 (the last coding exon) of RAD51B. Loss of function is an established disease mechanism for RAD51B, supported by germline literature identifying truncating mutations in breast cancer, ovarian cancer, and melanoma families. Under the ClinGen SVI PVS1 framework (PMC6185798), this variant is eligible for PVS1. However, the premature termination codon is in the last exon where nonsense-mediated decay is not predicted, and only 13 C-terminal amino acids (3.4% of the protein) are truncated. Per PMC6185798, nonsense variants in the last exon where NMD is not expected are assigned PVS1 at moderate strength.
Nonsense variant p.(Gln371Ter) in exon 11 (last exon) — no NMD expectedLoss of function is an established germline disease mechanism for RAD51BPMID:25600502 reports a germline RAD51B nonsense mutation (c.139C>T
PM2 supporting Pathogenic
This variant is present at an extremely low frequency in population databases. In gnomAD v4.1, it is observed at an allele frequency of 4.53 × 10⁻⁶ (6/1,324,198 alleles, 0 homozygotes), with the highest subpopulation frequency of 5.97 × 10⁻⁶ in the European (non-Finnish) population. The variant is absent from gnomAD v2.1 and gnomAD-Canada. This frequency is well below the 0.1% PM2 threshold for a dominant disorder.
gnomAD v4.1: AF = 4.53e-06 (6/1324198)
Assessed · not applied
Pathogenic
PS1 No prior pathogenic classification exists for the same amino acid change p.(Gln371Ter).
PS2 No de novo testing data are available for this variant.
PS3 No variant-specific functional data exist for NM_133509.4:c.1111C>T (p.Gln371Ter).
PS4 Prevalence of this variant in affected individuals versus controls is unknown.
PM1 The variant lies at residue 371 in the extreme C-terminal tail of RAD51B (384 amino acids), truncating only 13 C-terminal residues.
PM5 PM5 applies when a different pathogenic missense change has been identified at the same amino acid residue.
PM6 No de novo occurrence data are available for this variant.
PP1 No segregation data are available for this variant.
PP4 No patient phenotype data were provided for this case.
PP5 This variant is absent from ClinVar.
Benign
BA1 The gnomAD v4.1 allele frequency of 4.53 × 10⁻⁶ (0.00045%) is far below the 1% BA1 threshold.
BS1 The gnomAD v4.1 allele frequency of 4.53 × 10⁻⁶ (0.00045%) is far below the 0.3% BS1 threshold.
BS2 No homozygotes are observed in gnomAD (0/1,324,198 alleles).
BS3 No well-established functional studies showing no deleterious effect exist for this variant.
BS4 No segregation data are available for this variant.
BP2 No data are available regarding trans configuration with a known pathogenic RAD51B variant.
BP5 No alternative molecular basis for disease has been identified in this case, and BP5 is typically applied when an alternate cause is confirmed.
BP6 The variant is absent from ClinVar; no reputable source has classified it as benign.
N/A · 8 PM3 · PM4 · PP2 · PP3 · BP1 · BP3 · BP4 · BP7
Research & evidence
Population frequency
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
This variant is present in gnomAD v4.1 (AF= 4.53104e-06; MAF= 0.00045%, 6/1324198 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 5.97127e-06; MAF= 0.00060%, 6/1004812 alleles, homozygotes = 0); grpmax FAF= 2.15e-06.
v2.1
Absent from gnomAD v2.1.
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.00045% · 6 / 1,324,198
0 hom · FAF 0.00022%
European (non-Finnish)
6 / 1,004,812
0.0006%
+ 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
gnomAD v2.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
gnomAD Canada 🇨🇦
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
ClinVar screenshot
ClinVar
This variant is absent from ClinVar.
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.09). BayesDel score = 0.0486889.
Functional / OncoKB screenshot
Functional Likely Oncogenic
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Loss-of-function; curated oncogenicity label: Likely Oncogenic.
OncoKB ↗
COSMIC screenshot
COSMIC
Cancer hotspots screenshot
Cancer hotspots
Somatic evidence Not in COSMIC / hotspots
COSMIC
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
Hotspots
This variant does not lie in a statistically significant hotspot.
Sources & reference links
8Sources
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots
Triaged references · 5 PMIDs not cited in assessment
16778173 ↗ Haploinsufficiency of RAD51B causes centrosome fragmentation and aneuploidy in human cells. ONCOKB
24139550 ↗ Germline mutation in the RAD51B gene confers predisposition to breast cancer. ONCOKB
25368520 ↗ RAD51B Activity and Cell Cycle Regulation in Response to DNA Damage in Breast Cancer Cell Lines. ONCOKB
25600502 ↗ Germline RAD51B truncating mutation in a family with cutaneous melanoma. ONCOKB
26261251 ↗ Contribution of Germline Mutations in the RAD51B, RAD51C, and RAD51D Genes to Ovarian Cancer in the Population. ONCOKB