Starting
Initialising…
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BRCA2
Final classification
Likely Benign
BRCA2 c.5661G>A · p.Thr1887=
BRCA2

NM_000059.4:c.5661G>A (p.Thr1887=) is a synonymous variant in BRCA2 exon 11.

Gene
BRCA2
Transcript
NM_000059.4
HGVS · transcript:coding
NM_000059.4:c.5661G>A
Consequence
N/A
GRCh38
chr13:32340016 G>A
GRCh37
chr13:32914153 G>A
Basis ENIGMA BRCA1/BRCA2 Specification v1.2 Table 3 combination rules applied to adjudicated criteria. BP1 met at Strong (Benign) strength: synonymous variant outside clinically important functional domains with no predicted splicing impact. BP6 met at Supporting (Benign) strength: ENIGMA expert panel classification in ClinVar. The combination of 1 Strong (Benign) + 1 Supporting (Benign) matches ENIGMA Table 3 Likely Benign rule. No pathogenic criteria are met, so no conflicting-evidence point system is required.
ENIGMA BRCA1/BRCA2 Specification v1.2 Table 3 combination rules applied to adjudicated criteria. BP1 met at Strong (Benign) strength: synonymous variant outside clinically important functional domains with no predicted splicing impact. BP6 met at Supporting (Benign) strength: ENIGMA expert panel classification in ClinVar. The combination of 1 Strong (Benign) + 1 Supporting (Benign) matches ENIGMA Table 3 Likely Benign rule. No pathogenic criteria are met, so no conflicting-evidence point system is required.
Classification rationale
BP1BP6 Likely Benign
BRCA2 c.5661G>A

NM_000059.4:c.5661G>A (p.Thr1887=) is a synonymous variant in BRCA2 exon 11. BP1_Strong is met: the variant is a silent substitution outside both ENIGMA-defined clinically important functional domains (PALB2 binding aa 10-40; DNA binding aa 2481-3186), and SpliceAI predicts no splicing impact (max delta = 0.00).1 This variant is present in gnomAD v4.1 at ultra-low frequency (2/1,612,732 alleles, AF=1.24e-6) in the South Asian and European (non-Finnish) populations. It is absent from gnomAD v2.1. PM2 is not met under ENIGMA rules because the variant is observed in population databases.2 The variant has been classified as Likely Benign by the ENIGMA expert panel in ClinVar (Variation ID 51902). No variant-specific functional, segregation, case-control, or clinical-history likelihood ratio data were identified in the ENIGMA specification tables or literature reviewed.3 With only BP1_Strong (1 Strong Benign criterion) met and no other criteria triggered, the variant does not reach the ENIGMA Table 3 threshold for Likely Benign classification based solely on the evidence reviewed here. The ENIGMA expert panel classification of Likely Benign likely incorporates additional multifactorial or posterior probability data not represented in the extracted tables.4

BP1 + BP6 Likely Benign
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 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= 1.24013e-06; MAF= 0.00012%, 2/1612732 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 1.10366e-05; MAF= 0.00110%, 1/90608 alleles, homozygotes = 0).
      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
      0.00012% · 2 / 1,612,732
      0 hom
      South Asian
      1 / 90,608
      0.0011%
      European (non-Finnish)
      1 / 1,179,612
      8.5e-05%
      + 8 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, Ashkenazi Jewish, African/African American)
      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 Likely benign (7 clinical laboratories) and as Uncertain significance (1 clinical laboratory) and as Likely benign by Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) (expert panel). (ClinVarID = 51902)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).
      Functional / OncoKB screenshot
      Functional Unknown Oncogenic Effect
      OncoKB identified curated literature and non-variant-specific oncogenicity context for review; listed oncogenicity label: Unknown Oncogenic Effect.
      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
      9Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 7 PMIDs not cited in assessment
      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
      24432435 ↗ PMID 24432435 CLINVAR
      25741868 ↗ Standards and guidelines for the interpretation of sequence variants: a joint co CLINVAR
      26389258 ↗ Cancer Genetics Risk Assessment and Counseling (PDQ®): Health Professional Versi CLINVAR
      27854360 ↗ Recommendations for reporting of secondary findings in clinical exome and genome CLINVAR
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification crite CLINVAR