Starting
Initialising…
0%
BRCA2
Final classification
Pathogenic
BRCA2 c.5946del · p.Ser1982ArgfsTer22
BRCA2

NM_000059.4:c.5946del is a frameshift deletion in BRCA2 exon 11 resulting in a premature termination codon (p.Ser1982ArgfsTer22) with expected nonsense-mediated decay, in a gene where loss of function is an established mechanism for hereditary breast and ovarian cancer. Per ENIGMA Specifications Table 4, BRCA2 exon 11 PTC variants are assigned PVS1 at very strong weight.

Gene
BRCA2
Transcript
NM_000059.4
HGVS · transcript:coding
NM_000059.4:c.5946del
Consequence
N/A
GRCh38
chr13:32340300 GT>G
GRCh37
chr13:32914437 GT>G
Basis ENIGMA BRCA1/BRCA2 v1.2.0 Table 3 point system (+16: PVS1+8, PM5+4, PP4+4, PP5+1, BS1-1) meets pathogenic threshold >=10; all_of rule 1 Very Strong + >=1 Strong also independently satisfied.
ENIGMA BRCA1/BRCA2 v1.2.0 Table 3 point system (+16: PVS1+8, PM5+4, PP4+4, PP5+1, BS1-1) meets pathogenic threshold >=10; all_of rule 1 Very Strong + >=1 Strong also independently satisfied.
Classification rationale
PVS1PM5PP4PP5 BS1 Pathogenic
BRCA2 c.5946del

NM_000059.4:c.5946del is a frameshift deletion in BRCA2 exon 11 resulting in a premature termination codon (p.Ser1982ArgfsTer22) with expected nonsense-mediated decay, in a gene where loss of function is an established mechanism for hereditary breast and ovarian cancer. Per ENIGMA Specifications Table 4, BRCA2 exon 11 PTC variants are assigned PVS1 at very strong weight.1 ENIGMA Specifications Table 4 assigns PM5_Strong (PTC) to BRCA2 exon 11, indicating additional pathogenic weight for a protein termination codon variant in an exon where other proven pathogenic PTC variants have been previously observed.2 Clinical-history likelihood ratio analysis from Li et al. 2020 (PMID:31853058) yields an LR of 31.79 based on 149 carriers, exceeding the ENIGMA PP4_Strong threshold of ≥18.7:1. The personal and family cancer history profile of individuals carrying this variant is significantly enriched for breast and ovarian cancer compared to non-carriers.3 The variant is present in gnomAD population databases at low frequency in non-founder populations (grpmax FAF=5.39e-05 in v2.1, 2.154e-05 in v4.1), meeting ENIGMA BS1_Supporting (FAF >0.002% and ≤0.01%). The higher Ashkenazi Jewish allele frequency (0.589%) is attributable to a known founder effect and is excluded from BS1/BA1 assessment per ENIGMA non-founder population rules.4 This variant has been reported in ClinVar as Pathogenic by 67 clinical laboratories and by the ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel (ClinVar Variation ID: 9325). The variant has been observed in multiple affected individuals across diverse populations and has been described as a recurrent pathogenic founder mutation.5 Under ENIGMA Table 3 combining rules, the combination of PVS1 (Very Strong) + PM5 (Strong) satisfies the Pathogenic classification threshold (1 Very Strong + ≥1 Strong). PP4 (Strong) provides additional corroborating evidence. BS1_Supporting does not alter the pathogenic classification.6

PVS1 + PM5 + PP4 + PP5 + BS1 Pathogenic
1 vcep_specifications_table4_v1_2_2024_11_18cspec ↗pvs1_generic_framework ↗
2 vcep_specifications_table4_v1_2_2024_11_18cspec ↗
3 vcep_pmid_31853058_brca2_clinical_history_lrPMID:31853058 ↗
Gene diagram · NM_000059.4 · variants mapped to exon structure
BRCA2 NM_000059.4
Fetching transcript structure from UCSC…
Applied criteria · 5 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 pathogenic
      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= 0.000139416; MAF= 0.01394%, 225/1613878 alleles, homozygotes = 0) and has highest observed frequency in the Ashkenazi Jewish population (AF= 0.00533856; MAF= 0.53386%, 158/29596 alleles, homozygotes = 0); grpmax FAF= 2.154e-05.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 0.000276509; MAF= 0.02765%, 78/282088 alleles, homozygotes = 0) and has highest observed frequency in the Ashkenazi Jewish population (AF= 0.00588576; MAF= 0.58858%, 61/10364 alleles, homozygotes = 0); grpmax FAF= 5.39e-05.
      🇨🇦 CA
      This variant is absent from gnomAD-Canada.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.014% · 225 / 1,613,878
      0 hom · FAF 0.0022%
      Ashkenazi Jewish
      158 / 29,596
      0.53%
      Remaining individuals
      31 / 62,478
      0.05%
      European (non-Finnish)
      35 / 1,179,918
      0.003%
      African/African American
      1 / 74,912
      0.0013%
      + 6 not observed (Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian)
      gnomAD v2.1
      0.028% · 78 / 282,088
      0 hom · FAF 0.0054%
      Ashkenazi Jewish
      61 / 10,364
      0.59%
      Remaining individuals
      3 / 7,180
      0.042%
      European (non-Finnish)
      14 / 128,890
      0.011%
      + 5 not observed (African/African American, Admixed American, East Asian, European (Finnish), South Asian)
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Pathogenic (67 clinical laboratories) and as pathogenic (1 clinical laboratory) and as Pathogenic by ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel, ClinGen (expert panel). (ClinVarID = 9325)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).
      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 previously been reported in somatic cancers (COSMIC; COSV66447676, n = 10 times).
      Hotspots
      This variant does not lie in a statistically significant hotspot.
      Literature · how each cited paper was used
      1papers cited
      Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why. 9 further PMIDs triaged but not cited — see Sources & References.
      Li et al. 2020 BRCA1/2 clinical-history likelihood-ratio model
      Found
      Structured finding pending for this record — see source link.
      Applied to
      PP4 supports · met
      Sources & reference links
      8Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 9 PMIDs not cited in assessment
      10570174 ↗ Truncated BRCA2 is cytoplasmic: implications for cancer-linked mutations. ONCOKB
      11239455 ↗ BRCA2 is required for homology-directed repair of chromosomal breaks. ONCOKB
      20878484 ↗ A new mutation of BRCA2 gene in an Italian healthy woman with familial breast cancer history. ONCOKB
      22193408 ↗ BRCA1 and BRCA2: different roles in a common pathway of genome protection. ONCOKB
      24312913 ↗ A comprehensive focus on global spectrum of BRCA1 and BRCA2 mutations in breast cancer. ONCOKB
      10417300 ↗ De novo BRCA1 mutation in a patient with breast cancer and an inherited BRCA2 mutation. CLINVAR
      14559878 ↗ Shared genetic susceptibility to breast cancer, brain tumors, and Fanconi anemia. CLINVAR
      11466700 ↗ The frequency of founder mutations in the BRCA1, BRCA2, and APC genes in Australian Ashkenazi Jews: implications for the generality of U.S. population data. CLINVAR
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR