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BRCA2
Final classification
Uncertain Significance
BRCA2 c.7970A>C · p.Lys2657Thr
BRCA2

The BRCA2 c.7970A>C (p.Lys2657Thr, K2657T) variant has been reported in ClinVar, where the ClinGen ENIGMA expert panel classified it as uncertain significance and other submitters reported likely pathogenic and uncertain significance assertions.

Gene
BRCA2
Transcript
NM_000059.3
HGVS · transcript:coding
NM_000059.3:c.7970A>C
Consequence
N/A
GRCh38
chr13:32362687 A>C
GRCh37
chr13:32936824 A>C
Basis ENIGMA BRCA1 and BRCA2 Specification v1.2.0 Table 3 final-classification framework
ENIGMA BRCA1 and BRCA2 Specification v1.2.0 Table 3 final-classification framework
Classification rationale
PS3 Uncertain Significance
BRCA2 c.7970A>C

The BRCA2 c.7970A>C (p.Lys2657Thr, K2657T) variant has been reported in ClinVar, where the ClinGen ENIGMA expert panel classified it as uncertain significance and other submitters reported likely pathogenic and uncertain significance assertions.1 This variant is absent from gnomAD v2.1 and is present once in gnomAD v4.1 (1/1614028 alleles overall; highest observed frequency 1/59996 in Admixed American individuals), supporting rarity but not complete absence from population databases.2 In a calibrated BRCA2 functional study summarized by the ENIGMA BRCA1/2 specification, p.Lys2657Thr showed protein function similar to pathogenic control variants, supporting PS3 at strong strength.3 Computational evidence predicts no significant splice impact (SpliceAI max delta score 0.01), while the missense prediction profile is mixed under ENIGMA thresholds (REVEL 0.799; BayesDel 0.270216), so PP3 and BP4 are not independently met.4 A BRCA2 clinical-history likelihood ratio of 1.188967663938105 from 1 proband falls in the ENIGMA neutral zone (>0.48 and <2.08), so neither PP4 nor BP5 is supported by the reviewed multifactorial clinical-history data.5

PS3 Uncertain Significance
3 cspec ↗vcep_specifications_table9_v1_2_2024_11_18PMID:33609447 ↗
4 cspec ↗spliceai ↗revelbayesdel
5 cspec ↗vcep_pmid_31853058_brca2_clinical_history_lrPMID:31853058 ↗
Gene diagram · NM_000059.3 · variants mapped to exon structure
BRCA2 NM_000059.3
Fetching transcript structure from UCSC…
Applied criteria · 1 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
      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= 6.19568e-07; MAF= 0.00006%, 1/1614028 alleles, homozygotes = 0) and has highest observed frequency in the Admixed American population (AF= 1.66678e-05; MAF= 0.00167%, 1/59996 alleles, homozygotes = 0).
      v2.1
      Absent from gnomAD v2.1.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      6.2e-05% · 1 / 1,614,028
      0 hom
      Admixed American
      1 / 59,996
      0.0017%
      + 9 not observed (Remaining individuals, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American, European (non-Finnish))
      gnomAD v2.1
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Likely pathogenic (1 clinical laboratory) and as Uncertain significance (1 clinical laboratory) and as Uncertain Significance by ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel, ClinGen (expert panel).
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.799. BayesDel score = 0.270216.
      Functional / OncoKB screenshot
      Functional Unknown Oncogenic Effect
      OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. BRCA2, a tumor suppressor involved in the DNA damage response, is mutated in various cancer types.
      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.
      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.
      PMID PMID:33609447
      Found
      Structured finding pending for this record — see source link.
      Applied to
      PS3 supports · met
      Sources & reference links
      8Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots