Assessing Genetic Variants of Uncertain Significance: The Example of Breast Cancer

Abstract

Mutations in the BRCA1 or 2 genes can lead to an inherited increased risk of breast, ovarian and other cancers. Molecularly, these mutations manifest primarily as frameshift or nonsense mutations, leading to prematurely truncated proteins that would otherwise function as tumour suppressors. Up to 10–20% of all BRCA mutations are reported as variants of uncertain significance (VUS); these manifest as missense mutations (with resultant amino acid substitution), intronic variants with resultant effect on splicing capacity or in‐frame deletions and insertions, which may or may not change the reading frame of a gene. These variant sequences can confound rather than guide the risk assessment process in the genetic counselling of patients and family members, whether afflicted or not with an actual cancer. Several molecular methods are now able to discriminate those as yet unclassified variants between high and low risk for cancer development; databases have been generated accordingly and may allow some further prediction of the probability of deleterious behaviour.

This article aims to clarify the clinical relevance of BRCA VUS, to assimilate resources and make suggestions for estimating their clinical impact, and to highlight the need for further studies in this area.

Key Concepts:

  • There are limited guidelines for the specific management and surveillance of patients and their family members who harbour genetic variants of uncertain significance.

  • Integrated models to discriminate high‐risk from low‐risk variants have been generated.

  • Application of these models is considered.

  • Further clinical trials for risk management are advocated.

  • Up to 20% of BRCA 1 and 2 mutations can be missense mutations which amount to variants of uncertain significance, the deleterious nature of which are unclear in clinical practice.

Keywords: BRCA; genetic variants; genetic counselling; VUS; BRCA 1; BRCA 2

Figure 1.

A schema of multifaceted determination of classification of BRCA VUSs by contribution of multiple molecular methods approach to use for BRCA‐VUS clinical classification. Reproduced from Calo et al., Figure 1, p. 1653, with permission from Cancers (Open Access journal). © Creative Commons Attribution Licence.

Figure 2.

Flow model representing methods that contribute to estimation of classes of risk of clinical impact of BRCA VUSs (Calo et al., ). Literature suggests to then counsel as if no mutation was detected for Class 1 and 2 and not to use the information as predictive testing in at‐risk relatives; for Class 3, to counsel on the basis of family history and other risk factors but not to use this classification as predictive testing in high‐risk relatives; and to engage full high‐risk surveillance for Class 4 and 5 and to test at‐risk relatives for the variant (Lindor et al., ). Reproduced from Calo et al., Figure 2, p. 1654, with permission from Cancers (Open Access journal). © Creative Commons Attribution Licence.

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Morris, Gloria J(Dec 2013) Assessing Genetic Variants of Uncertain Significance: The Example of Breast Cancer. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0025220]