Starting
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BRCA2
Final classification
Likely Pathogenic
BRCA2 c.9117+2T>C · p.?
BRCA2

NM_000059.3:c.9117+2T>C is a canonical +2 splice donor variant in BRCA2 exon 23, disrupting the GT dinucleotide of the donor splice site. ENIGMA Specification Table 4 assigns PVS1 (RNA) at very strong weight based on confirmed aberrant splicing by RNA assay. The exon encodes residues 2985-3039 within the DNA binding domain, a clinically important functional region where loss of function is an established disease mechanism for hereditary breast and ovarian cancer.

Gene
BRCA2
Transcript
NM_000059.3
HGVS · transcript:coding
NM_000059.3:c.9117+2T>C
Consequence
N/A
GRCh38
chr13:32379915 T>C
GRCh37
chr13:32954052 T>C
Basis ENIGMA BRCA1/BRCA2 VCEP Specification v1.2.0, Table 3 combination rules applied to adjudicated criteria. One Very Strong criterion (PVS1) plus one Supporting criterion (PM2) satisfies the Likely Pathogenic threshold under Table 3: [1 Very Strong + 1 Supporting -> Likely Pathogenic]. ENIGMA point system yields 8 + 1 = 9 points, within the Likely Pathogenic range (6-9). No benign criteria are met, so no conflicting evidence.
ENIGMA BRCA1/BRCA2 VCEP Specification v1.2.0, Table 3 combination rules applied to adjudicated criteria. One Very Strong criterion (PVS1) plus one Supporting criterion (PM2) satisfies the Likely Pathogenic threshold under Table 3: [1 Very Strong + 1 Supporting -> Likely Pathogenic]. ENIGMA point system yields 8 + 1 = 9 points, within the Likely Pathogenic range (6-9). No benign criteria are met, so no conflicting evidence.
Classification rationale
PVS1PM2 Likely Pathogenic
BRCA2 c.9117+2T>C

NM_000059.3:c.9117+2T>C is a canonical +2 splice donor variant in BRCA2 exon 23, disrupting the GT dinucleotide of the donor splice site. ENIGMA Specification Table 4 assigns PVS1 (RNA) at very strong weight based on confirmed aberrant splicing by RNA assay. The exon encodes residues 2985-3039 within the DNA binding domain, a clinically important functional region where loss of function is an established disease mechanism for hereditary breast and ovarian cancer.1 The variant is absent from gnomAD v2.1 and v4.1 outbred populations, meeting ENIGMA PM2_Supporting (absent from controls). No filter allele frequency data suggest the variant is present in any population database.2 No formal case-control study (PS4), co-segregation analysis (PP1), or clinical-history likelihood ratio (PP4/BP5) meeting ENIGMA quantitative thresholds is available. The variant is not listed in the Li et al. 2020 BRCA2 clinical-history LR table (PMID:31853058). ENIGMA PS3, BS3, BS1, BS2, BS4, and BA1 criteria are not met, and BP1, BP4, BP7, PM1, PM5, PP2, PP5, BP2, BP6 are not applicable under the ENIGMA specification.3 Under ENIGMA Table 3 combining rules, one Very Strong criterion (PVS1) and one Supporting criterion (PM2) is sufficient for a Likely Pathogenic classification.4

PVS1 + PM2 Likely Pathogenic
1 vcep_specifications_table4_v1_2_2024_11_18cspec ↗
3 vcep_pmid_31853058_brca2_clinical_history_lrcspec ↗
Gene diagram · NM_000059.3 · variants mapped to exon structure
BRCA2 NM_000059.3
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.
      🇨🇦 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 has been reported in ClinVar as Pathogenic (1 clinical laboratory). (ClinVarID = 267714)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). BayesDel score = 0.321175.
      Functional No data
      No calibrated functional assay or RNA evidence was identified for this variant.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Somatic evidence
      COSMIC
      This variant has not previously been reported in somatic cancers (COSMIC).
      Hotspots
      This variant does not lie in a statistically significant cancer hotspot.
      COSMIC ↗
      Sources & reference links
      8Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC
      Triaged references · 8 PMIDs not cited in assessment
      23918944 ↗ Tamoxifen and risk of contralateral breast cancer for BRCA1 and BRCA2 mutation carriers. CLINVAR
      15604628 ↗ Genetic cancer risk assessment and counseling: recommendations of the national society of genetic counselors. CLINVAR
      17392385 ↗ American Cancer Society guidelines for breast screening with MRI as an adjunct to mammography. CLINVAR
      17508274 ↗ Risk assessment and genetic counseling for hereditary breast and ovarian cancer: recommendations of the National Society of Genetic Counselors. CLINVAR
      19305347 ↗ ACOG Practice Bulletin No. 103: Hereditary breast and ovarian cancer syndrome. CLINVAR
      20065170 ↗ American Society of Clinical Oncology policy statement update: genetic and genomic testing for cancer susceptibility. CLINVAR
      20301425 ↗ BRCA1- and BRCA2-Associated Hereditary Breast and Ovarian Cancer. CLINVAR
      23188549 ↗ NSGC practice guideline: risk assessment and genetic counseling for hereditary breast and ovarian cancer. CLINVAR