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RAD51B
Final classification
Likely Benign
RAD51B c.476G>A · p.Arg159His
RAD51B

NM_133509.4:c.476G>A (p.Arg159His) in RAD51B is classified as Likely benign based on three supporting benign criteria per the generic ACMG/AMP 2015 framework (PMID:25741868). The generic ACMG combination rules require ≥2 supporting benign criteria for Likely benign classification.

Gene
RAD51B
Transcript
NM_133509.4
HGVS · transcript:coding
NM_133509.4:c.476G>A
Consequence
N/A
GRCh38
chr14:67885892 G>A
GRCh37
chr14:68352609 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: BS1 supporting, BP4 supporting, BP6 supporting; combination = 3 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: BS1 supporting, BP4 supporting, BP6 supporting; combination = 3 supporting benign, which maps to Likely Benign.
Classification rationale
BS1BP4BP6 Likely Benign
RAD51B c.476G>A

NM_133509.4:c.476G>A (p.Arg159His) in RAD51B is classified as Likely benign based on three supporting benign criteria per the generic ACMG/AMP 2015 framework (PMID:25741868). The generic ACMG combination rules require ≥2 supporting benign criteria for Likely benign classification.1 The variant exceeds the 0.3% BS1 allele frequency threshold in the South Asian subpopulation (gnomAD v2.1 SAS AF = 0.358%, 109/30,430 alleles, 1 homozygote; gnomAD v4.1 SAS AF = 0.337%, 305/90,530 alleles, 3 homozygotes; grpmax FAF = 0.303%), indicating it is too common to be a highly penetrant pathogenic variant (BS1_supporting).2 Multiple in silico tools predict a benign impact: REVEL score 0.385 (below 0.5 threshold), BayesDel score 0.129 (near-zero), and SpliceAI max delta 0.00 (no splice impact), meeting BP4_supporting.3 ClinVar reports this variant as Likely benign from three clinical testing laboratories (Ambry Genetics, PreventionGenetics, NHLS; Variation ID 1678949), meeting BP6_supporting.4 No pathogenic or likely pathogenic criteria were met. PVS1 does not apply to this missense variant. PS3/PS4 are not met due to absence of variant-specific functional or case-control data. PM2 is not met as the variant frequency exceeds 0.1% in the South Asian population. PP3 is not met because all in silico tools predict a benign effect. PP5 is not met as ClinVar reports Likely benign, not pathogenic.

BS1 + BP4 + BP6 Likely Benign
1 generic_acmg_combination_rules
3 revelbayesdelspliceai ↗
Gene diagram · NM_133509.4 · variants mapped to exon structure
RAD51B NM_133509.4
Fetching transcript structure from UCSC…
Applied criteria · 3 met · select any tile
Met
Not met
Not assessed
N/A
Strength very strong supporting
Pathogenic evidence
PVS
PS
PM
PP
Benign evidence
BA
BS
BP
Rationale
Select a criterion.
Sources
Evidence used
    Gaps remaining
      Rule
      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= 0.000238735; MAF= 0.02387%, 384/1608480 alleles, homozygotes = 3) and has highest observed frequency in the South Asian population (AF= 0.00336905; MAF= 0.33690%, 305/90530 alleles, homozygotes = 3); grpmax FAF= 0.00305752.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 0.000418624; MAF= 0.04186%, 118/281876 alleles, homozygotes = 1) and has highest observed frequency in the South Asian population (AF= 0.00358199; MAF= 0.35820%, 109/30430 alleles, homozygotes = 1); grpmax FAF= 0.00303643.
      🇨🇦 CA
      This variant is present in gnomAD-Canada v1.0 (AF= 0.0006515365403409708, 12/18418 alleles, homozygotes = 0).
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.024% · 384 / 1,608,480
      3 hom · FAF 0.31%
      South Asian
      305 / 90,530
      0.34%
      3 hom
      Remaining individuals
      18 / 62,184
      0.029%
      Admixed American
      14 / 59,870
      0.023%
      Middle Eastern
      1 / 6,028
      0.017%
      European (non-Finnish)
      43 / 1,176,150
      0.0037%
      European (Finnish)
      2 / 63,862
      0.0031%
      East Asian
      1 / 44,766
      0.0022%
      + 3 not observed (Amish, Ashkenazi Jewish, African/African American)
      gnomAD v2.1
      0.042% · 118 / 281,876
      1 hom · FAF 0.3%
      South Asian
      109 / 30,430
      0.36%
      1 hom
      Remaining individuals
      2 / 7,188
      0.028%
      Admixed American
      4 / 35,218
      0.011%
      European (Finnish)
      2 / 25,080
      0.008%
      European (non-Finnish)
      1 / 128,786
      0.00078%
      + 3 not observed (African/African American, Ashkenazi Jewish, East Asian)
      gnomAD Canada 🇨🇦
      0.065% · 12 / 18,418
      0 hom · FAF 0.51%
      South Asian
      12 / 1,362
      0.88%
      + 8 not observed (African/African American, Latino/Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), Middle Eastern, European (non-Finnish), Remaining individuals)
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Likely benign (3 clinical laboratories). (ClinVarID = 1678949)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.385. BayesDel score = 0.129411.
      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; COSV66846898, 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
      Triaged references · 6 PMIDs not cited in assessment
      23918944 ↗ Tamoxifen and risk of contralateral breast cancer for BRCA1 and BRCA2 mutation carriers. CLINVAR
      25741868 ↗ Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. CLINVAR
      17392385 ↗ American Cancer Society guidelines for breast screening with MRI as an adjunct to mammography. CLINVAR
      20301425 ↗ BRCA1- and BRCA2-Associated Hereditary Breast and Ovarian Cancer. CLINVAR
      23788249 ↗ ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing. CLINVAR
      26324357 ↗ American Society of Clinical Oncology Policy Statement Update: Genetic and Genomic Testing for Cancer Susceptibility. CLINVAR