Reclassification of Variants of Uncertain Significance in BRCA1, BRCA2, and PALB2: Implications for Clinical Decision-Making in Breast Cancer

Technical Summary: Reclassification of Variants of Uncertain Significance in BRCA1, BRCA2, and PALB2

Problem Statement
The clinical management of breast cancer relies heavily on the identification of germline pathogenic variants in high-penetrance susceptibility genes, specifically BRCA1, BRCA2, and PALB2. These findings dictate risk stratification, surveillance strategies, and therapeutic decisions, including the use of PARP inhibitors and risk-reducing surgeries. However, the widespread adoption of next-generation sequencing (NGS) multigene panels has led to a significant increase in the detection of Variants of Uncertain Significance (VUS). By definition, VUS lack sufficient evidence to classify them as pathogenic or benign, rendering them clinically unactionable under current guidelines. This creates a substantial burden of uncertainty for patients and clinicians, often resulting in anxiety, ambiguous counseling, and the inability to utilize targeted therapies or preventive interventions based solely on these findings. The core challenge addressed is the need to resolve these uncertainties through the re-evaluation of VUS as new evidence becomes available.

Methodology
This study presents a retrospective analysis of 6,369 breast cancer patients who underwent 52-gene NGS panel testing at Genekor Medical S.A. between January 1, 2020, and December 31, 2024. The cohort included patients who tested negative for pathogenic or likely pathogenic variants but harbored at least one VUS.

The researchers focused specifically on VUS identified within the three high-risk genes: BRCA1, BRCA2, and PALB2. A total of 436 VUS were identified in these genes (105 in BRCA1, 257 in BRCA2, and 74 in PALB2). These variants were retrospectively re-evaluated using the American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) classification framework, augmented by gene-specific criteria established by the ClinGen Variant Curation Expert Panel (VCEP).

The reclassification process integrated multiple data sources, including:

• Updated population frequency data.
• Publicly available databases and VCEP documentation.
• Unpublished internal laboratory data.
• Functional evidence and segregation data from the scientific literature.
• Internal laboratory observations collected during the study period.

Key Results
The study identified a reclassification rate of 3.0% among the 436 VUS in BRCA1, BRCA2, and PALB2. Specifically:

• Total Reclassified: 13 variants.
• Upgraded to Likely Pathogenic (LP): 3 variants (0.69% of the total VUS cohort).
  • Two were in BRCA1 (representing 1.9% of BRCA1 VUS).
  • One was in BRCA2 (representing 0.39% of BRCA2 VUS).
  • No PALB2 variants were upgraded.
• Downgraded to Likely Benign (LB): 10 variants (2.3% of the total VUS cohort).
  • Six were in BRCA1 (5.7% of BRCA1 VUS).
  • Three were in BRCA2 (1.17% of BRCA2 VUS).
  • One was in PALB2 (1.35% of PALB2 VUS).

The data indicates a predominance of downgrading over upgrading, a trend consistent with previous studies suggesting that the majority of reclassified VUS ultimately prove to be non-pathogenic as evidence accumulates.

Significance and Claims
The paper asserts that while the absolute reclassification rate is low (3%), the clinical impact of these changes is substantial. The authors highlight two primary dimensions of significance:

1. Therapeutic and Surgical Implications: Variants reclassified as Likely Pathogenic can alter patient management by rendering individuals eligible for targeted systemic therapies (e.g., PARP inhibitors) and influencing decisions regarding risk-reducing surgical interventions and intensified surveillance.
2. Psychosocial and Clinical Relief: The reclassification of VUS to Likely Benign is critical for reducing patient anxiety and preventing unnecessary medical procedures. The authors note that patients with VUS often overestimate their cancer risk; resolving these uncertainties allows for more accurate risk communication and avoids overtreatment.

The study concludes that the reclassification of VUS is an essential component of precision oncology, bridging the gap between genetic findings and clinical action. It underscores the necessity of ongoing variant reinterpretation, longitudinal genetic counseling, and the integration of evolving genomic evidence into clinical practice to optimize patient care and reduce the psychological burden associated with hereditary cancer risk.