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Initialising…
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BRCA2
Final classification
Pathogenic
BRCA2 c.29_63del · p.Thr10SerfsTer9
BRCA2

The BRCA2 c.29_63del (p.(Thr10SerfsTer9)) variant has not been observed in somatic cancers in COSMIC and has not been reported in ClinVar; OncoKB classifies p.(T10Sfs*9) as Likely Oncogenic with a likely loss-of-function effect.

Gene
BRCA2
Transcript
NM_000059.4
HGVS · transcript:coding
NM_000059.4:c.29_63del
Consequence
N/A
GRCh38
chr13:32316486 CAACATTTTTTGAAATTTTTAAGACACGCTGCAACA>C
GRCh37
chr13:32890623 CAACATTTTTTGAAATTTTTAAGACACGCTGCAACA>C
Basis ENIGMA BRCA1 and BRCA2 Specification v1.2 Table 3 criteria-combination framework (official CSPEC/VCEP final-classification framework).
ENIGMA BRCA1 and BRCA2 Specification v1.2 Table 3 criteria-combination framework (official CSPEC/VCEP final-classification framework).
Classification rationale
PVS1PM5 Pathogenic
BRCA2 c.29_63del

The BRCA2 c.29_63del (p.(Thr10SerfsTer9)) variant has not been observed in somatic cancers in COSMIC and has not been reported in ClinVar; OncoKB classifies p.(T10Sfs*9) as Likely Oncogenic with a likely loss-of-function effect.1 This variant is absent from gnomAD v2.1 and gnomAD v4.1, so the observed allele frequency is 0 in the queried population datasets.2 The deletion causes an early frameshift with premature termination in exon 2, and ENIGMA BRCA2 Table 4 assigns exon 2 protein-truncating variants PVS1 and PM5_Strong (PTC), which supports a loss-of-function disease mechanism for this variant.3 SpliceAI predicts no significant splice impact for this variant, with a maximum delta score of 0.04.4

PVS1 + PM5 Pathogenic
3 cspec ↗pvs1_gene_contextpvs1_variant_assessmentvcep_s_p_e_c_i_f_i_c_a_t_i_o_n_s___t_a_b_l_e_4___v_1___2___2_0_2_4___1_1___1_8
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 = 0.04).
      Functional / OncoKB screenshot
      Functional Likely Oncogenic
      OncoKB classifies this variant as Likely Oncogenic; biological effect: Likely Loss-of-function.
      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