Starting
Initialising…
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BRCA2
Final classification
Pathogenic
BRCA2 c.1924_1925insGG · p.Ser642TrpfsTer3
BRCA2

The BRCA2 c.1924_1925insGG (p.(Ser642TrpfsTer3), p.(S642Wfs*3)) variant has not been observed in somatic cancers in COSMIC and has not been reported in ClinVar.

Gene
BRCA2
Transcript
NM_000059.4
HGVS · transcript:coding
NM_000059.4:c.1924_1925insGG
Consequence
N/A
GRCh38
chr13:32336279 T>TGG
GRCh37
chr13:32910416 T>TGG
Basis ENIGMA BRCA1/BRCA2 Specification v1.2 Table 3 final-classification framework (CSPEC/VCEP criteria-combination rules)
ENIGMA BRCA1/BRCA2 Specification v1.2 Table 3 final-classification framework (CSPEC/VCEP criteria-combination rules)
Classification rationale
PVS1PM5 Pathogenic
BRCA2 c.1924_1925insGG

The BRCA2 c.1924_1925insGG (p.(Ser642TrpfsTer3), p.(S642Wfs*3)) variant has not been observed in somatic cancers in COSMIC and has not been reported in ClinVar.1 This variant is absent from gnomAD v2.1 and gnomAD v4.1, supporting rarity in population databases.2 This early frameshift predicts premature truncation of BRCA2, and the ENIGMA BRCA2 specification supports full PVS1 weight with additional PM5_Strong (PTC) applicability for truncating variants in exon 11.3 SpliceAI predicts no significant splice impact for this variant (max delta score 0.01), which is below the ENIGMA PP3 splice threshold of 0.2 and supports a truncating rather than splice-altering mechanism.4

PVS1 + PM5 Pathogenic
3 cspec ↗pvs1_gene_contextpvs1_variant_assessmentvcep_specifications_table4_v1_2_2024_11_18
Gene diagram · NM_000059.4 · variants mapped to exon structure
BRCA2 NM_000059.4
Fetching transcript structure from UCSC…
Applied criteria · 2 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
      Absent from gnomAD v4.1.
      v2.1
      Absent from gnomAD v2.1.
      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.
      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 = 0.01).
      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
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 5 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