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RAD51B
Final classification
Likely Benign
RAD51B c.121G>A · p.Val41Met
RAD51B

NM_133509.4:c.121G>A (p.Val41Met) is a missense variant in RAD51B, a gene in which loss-of-function truncating variants are the established germline disease mechanism for melanoma and breast/ovarian cancer predisposition.

Gene
RAD51B
Transcript
NM_133509.4
HGVS · transcript:coding
NM_133509.4:c.121G>A
Consequence
N/A
GRCh38
chr14:67825500 G>A
GRCh37
chr14:68292217 G>A
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: PM2 supporting, BP1 supporting, BP4 supporting; combination = 1 supporting + 2 supporting benign, which maps to Likely Benign.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM2 supporting, BP1 supporting, BP4 supporting; combination = 1 supporting + 2 supporting benign, which maps to Likely Benign.
Classification rationale
PM2 BP1BP4 Likely Benign
RAD51B c.121G>A

NM_133509.4:c.121G>A (p.Val41Met) is a missense variant in RAD51B, a gene in which loss-of-function truncating variants are the established germline disease mechanism for melanoma and breast/ovarian cancer predisposition.1 This variant is extremely rare in population databases: present at an allele frequency of 6.20e-07 in gnomAD v4.1 (1/1,613,612 alleles) and absent from gnomAD v2.1 and gnomAD-Canada, meeting PM2 at supporting strength.2 Multiple in silico predictors are concordant for a benign effect: REVEL score 0.039 (benign), BayesDel score -0.491 (benign), and SpliceAI max delta 0.13 (no splice impact), meeting BP4 at supporting strength.3 As a missense variant in a gene where truncating variants are the primary pathogenic mechanism, BP1 applies at supporting strength. The variant is absent from ClinVar; no functional studies, segregation data, case-control data, or de novo observations are available. No publications specifically mention NM_133509.4:c.121G>A.4 With one supporting pathogenic criterion (PM2) and two supporting benign criteria (BP1, BP4), the net evidence is insufficient to classify this variant as either pathogenic or benign. The variant is classified as a Variant of Uncertain Significance (VUS).5

PM2 + BP1 + BP4 Likely Benign
1 pvs1_gene_context
3 revelbayesdelspliceai ↗
5 generic_acmg_combination_rules
Gene diagram · NM_133509.4 · variants mapped to exon structure
RAD51B NM_133509.4
Fetching transcript structure from UCSC…
Applied criteria · 3 applied · 19 assessed
Applied · 3
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
Extremely low population frequency: gnomAD v4.1 AF = 6.20e-07 (1/1,613,612 alleles, no homozygotes). Absent from gnomAD v2.1 and gnomAD-Canada. Well below the 0.1% PM2 threshold for rare diseases.
gnomAD v4.1: 1 allele out of 1613612 (AF = 6.20e-07)
BP1 supporting Benign
Missense variant (p.Val41Met) in RAD51B, a gene in which loss-of-function truncating variants are the established germline disease mechanism. Published germline RAD51B mutations associated with melanoma and breast/ovarian cancer predisposition are predominantly truncating or splice-disrupting.
RAD51B germline disease mechanism: loss-of-function via truncating variants (PMID:25600502)Published germline RAD51B mutations are predominantly nonsense and splicing variants
BP4 supporting Benign
Multiple lines of computational evidence suggest no impact on gene product: REVEL score 0.039 (benign), BayesDel score -0.491 (benign), and SpliceAI max delta 0.13 (no significant splice impact). All in silico predictors are concordant for a benign effect.
REVEL: 0.039 (benignwell below ~0.5 threshold)BayesDel: -0.491 (negative score
Assessed · not applied
Pathogenic
PS1 No pathogenic missense variant at the same amino acid position has been established in ClinVar or the literature to support PS1.
PS2 No de novo data are available for this variant.
PS3 No functional studies have been reported for NM_133509.4:c.121G>A (p.Val41Met).
PS4 No case-control or enrichment data are available for this variant.
PM1 Residue 41 does not lie within a statistically significant mutational hotspot (cancerhotspots.org).
PM6 No de novo data are available for this variant.
PP1 No co-segregation data are available for this variant.
PP2 No gene-level constraint data (e.g., missense Z-score, o/e ratio) are available to assess whether RAD51B has a low rate of benign missense variation.
PP3 Multiple in silico predictors support a benign impact: REVEL score 0.039 (well below pathogenic threshold of ~0.5), BayesDel score -0.491 (negative, predicting benign), SpliceAI max delta 0.13 (no significant splice impact).
PP4 No patient phenotype or family history data are available to assess disease specificity.
PP5 Absent from ClinVar; no reputable source has reported NM_133509.4:c.121G>A as pathogenic.
Benign
BA1 gnomAD v4.1 allele frequency is 6.20e-07, far below the 1% BA1 threshold for standing benign variation.
BS1 gnomAD v4.1 allele frequency is 6.20e-07, far below the 0.3% BS1 threshold for benign standing variation in rare disease genes.
BS2 No data are available regarding observation in healthy adults independent of disease status.
BS3 No experimental functional studies demonstrating a neutral effect have been reported for this variant.
BS4 No segregation data are available to assess lack of segregation with disease.
BP2 No data are available regarding observation in trans with a pathogenic dominant variant.
BP5 No alternate molecular basis for disease has been identified in this case.
BP6 Absent from ClinVar; no reputable source has reported NM_133509.4:c.121G>A as benign.
N/A · 3 PVS1 · PM5 · BP7
Research & evidence
Population frequency · supports benign
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= 6.19728e-07; MAF= 0.00006%, 1/1613612 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 8.4762e-07; MAF= 0.00008%, 1/1179774 alleles, homozygotes = 0).
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
6.2e-05% · 1 / 1,613,612
0 hom
European (non-Finnish)
1 / 1,179,774
8.5e-05%
+ 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 = 0.13). REVEL score = 0.039. BayesDel score = -0.491014.
Functional / OncoKB screenshot
Functional Unknown Oncogenic Effect
OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. RAD51B, a DNA repair protein involved in homologous recombination, is altered by mutation in various cancer types.
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