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RAD51B
Final classification
Likely Benign
RAD51B c.481C>T · p.Pro161Ser
RAD51B

NM_133509.3:c.481C>T (p.Pro161Ser) is absent from gnomAD v2.1 and v4.1, meeting PM2 at supporting strength.

Gene
RAD51B
Transcript
NM_133509.3
HGVS · transcript:coding
NM_133509.3:c.481C>T
Consequence
N/A
GRCh38
chr14:67885897 C>T
GRCh37
chr14:68352614 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: PM2 supporting, BP1 supporting benign, BP4 supporting benign; 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 benign, BP4 supporting benign; combination = 1 supporting + 2 supporting benign, which maps to Likely Benign.
Classification rationale
PM2 BP1BP4 Likely Benign
RAD51B c.481C>T

NM_133509.3:c.481C>T (p.Pro161Ser) is absent from gnomAD v2.1 and v4.1, meeting PM2 at supporting strength.1 The variant is a missense change in RAD51B, a gene where the established disease mechanism is loss-of-function via truncating variants. Published germline RAD51B pathogenic variants are nonsense or splice-site mutations (PMID:25600502), and systematic screening of RAD51B found no pathogenic missense variants in breast cancer families (PMID:21533530). BP1 is met at supporting benign strength. Multiple in silico tools predict a benign effect: REVEL score 0.289, BayesDel score -0.077, and SpliceAI max delta 0.11. BP4 is met at supporting benign strength.2 The variant is absent from ClinVar; no classification or functional evidence exists for this variant in the literature. OncoKB reports unknown oncogenic effect, and COSMIC reports the variant in somatic cancers (n=2) without functional characterization.3 Applying generic ACMG/AMP 2015 combination rules (PMID:25741868): with two supporting benign criteria (BP1, BP4) and one supporting pathogenic criterion (PM2), the evidence weighs in favor of a benign interpretation, meeting the threshold for Likely Benign.4

PM2 + BP1 + BP4 Likely Benign
2 revelbayesdelspliceai ↗
4 generic_acmg_combination_rules
Gene diagram · NM_133509.3 · variants mapped to exon structure
RAD51B NM_133509.3
Fetching transcript structure from UCSC…
Applied criteria · 3 applied · 20 assessed
Applied · 3
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
NM_133509.3:c.481C>T is absent from gnomAD v2.1 and gnomAD v4.1, meeting the generic ACMG PM2 threshold (allele frequency <0.1% in population databases).
Absent from gnomAD v2.1v4.1and gnomAD-Canada v1.0.
BP1 supporting Benign
NM_133509.3:c.481C>T (p.Pro161Ser) is a missense variant in RAD51B, a gene for which the established disease mechanism is loss-of-function via truncating variants. The published literature documents germline nonsense and splice-site mutations as pathogenic, while missense variants are not a well-established disease mechanism for this gene (PMID:25600502, PMID:21533530).
RAD51B disease mechanism is truncating LOF. PMID:25600502 reports a germline nonsense mutation as pathogenic. PMID:21533530 finds no truncating mutations and concludes RAD51B is unlikely a high-penetrance gene.
BP4 supporting Benign
Multiple lines of computational evidence predict no impact on gene product: REVEL score 0.289 (below 0.5 threshold), BayesDel score -0.077 (negative score indicates benign), and SpliceAI max delta score 0.11 (below 0.2 threshold, no predicted splice alteration).
REVEL 0.289BayesDel -0.077SpliceAI max delta 0.11 — all three in silico tools predict a benign effect.
Assessed · not applied
Pathogenic
PS1 No known pathogenic variant at codon 161 with the same amino acid change (p.Pro161Ser) has been identified.
PS2 No de novo evidence is available.
PS3 No variant-specific functional studies were identified.
PS4 No case-control or cohort prevalence data are available.
PM1 Residue 161 (Pro) is not located in a statistically significant mutational hotspot per cancerhotspots.org.
PM5 No pathogenic missense variant at codon 161 of RAD51B was identified in ClinVar.
PM6 No assumed de novo evidence is available.
PP1 No co-segregation data are available.
PP2 RAD51B disease mechanism is loss-of-function via truncating variants; missense variation is not a well-established disease mechanism for this gene.
PP3 Multiple in silico tools predict a benign effect: REVEL score 0.289 (below 0.5 threshold), BayesDel score -0.077 (negative score indicates benign), SpliceAI max delta 0.11 (below 0.2 threshold).
PP4 No patient phenotype or clinical history was provided.
PP5 The variant is absent from ClinVar.
Benign
BA1 Variant is absent from gnomAD v2.1 and v4.1.
BS1 Variant is absent from gnomAD.
BS2 No data on observation in healthy adult controls or unaffected individuals are available.
BS3 No well-established in vitro or in vivo functional studies demonstrate no damaging effect for p.Pro161Ser.
BS4 No segregation data are available to demonstrate lack of co-segregation with disease in affected family members.
BP2 No phasing data are available.
BP5 No information about an alternate molecular basis for disease in this case is available.
BP6 The variant is absent from ClinVar.
N/A · 5 PVS1 · PM3 · PM4 · BP3 · BP7
Research & evidence
Population frequency · supports benign
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
Absent from gnomAD v4.1.
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
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
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 = 0.11). REVEL score = 0.289. BayesDel score = -0.0772252.
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 previously been reported in somatic cancers (COSMIC; COSV66849284, n = 2 times).
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