Variants of uncertain significance (VUS) are an aspect of genetic testing that is often seen as a challenge. How do I explain this result to my patient? Does this result change how I manage a patient? Senior Geneticist Jennifer Schleit described why variants are classified as a VUS and what can be done to advance reclassification.
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What if it’s a VUS?
The classification of genetic variants, based on the ACMG guidelines, is usually a five-tiered scheme which describes the quantity and quality of evidence needed to classify the variant as pathogenic, likely pathogenic, a variant of uncertain significance (VUS), likely benign, or benign. If the classification of the variant is as a VUS, it means that, at the time of interpretation, there was not sufficient evidence to determine if the variant is related to disease or not.
“It might be that the variant in question is rare, but has not been identified in affected individuals. Or the identified variant may be a different mechanism than is known for that gene. For example, a deletion in genes where only gain of function has been reported. Therefore, we cannot be sure if the variant in question has any clinical significance,” Schleit said.
If the variant has been reported in individuals who are affected with disease, but the variant is also seen in a large number of healthy control individuals, it is often difficult to determine whether this represents reduced penetrance of the variant or if the variant is a common benign variant that has been identified in clinical genetic testing and is being falsely attributed to a phenotype.
“According to the ACMG guidelines, a VUS should not be used in clinical decision-making. If a patient is identified to have a VUS, all clinical decisions should be based on personal and family history and not on the presence of the VUS,” Schleit underlined.
Schleit further emphasized that ACMG does recommend pursuing follow-up testing to generate additional evidence that may allow for reclassification of these variants.
“We may not understand the clinical significance of a variant right now, but there is a very real possibility that variant is the explanation for the patient.”
What can I do to help with reclassification?
Over time, as more evidence becomes available, variants can be reclassified.
“Patients with a similar phenotype may be identified with that same variant. This would be additional evidence that could then be used to support the reclassification,” Schleit said.
In addition, family segregation studies may provide evidence to support reclassification.
“Also, sequencing of normal cohorts from previously untested ethnic or geographic populations, completing functional studies or additional variants of the same type are discovered can all support reclassification,” Schleit listed.
Schleit said that reclassification is a collaborative process between the laboratory and the clinician.
“To begin with, clinical information about the patient, including detailed phenotype information and the relevant family medical history, is very important to clinical interpretation,” Schleit said.
“It is beneficial to look at the family history to see if segregation studies could be informative. Is the family history consistent with the inheritance type for that gene? Are there other affected and unaffected family members that could be tested?,” Schleit listed.
Also, distantly related affected individuals can provide really strong evidence. If you have individuals who are cousins and you can show that there is segregation between the two individuals of the phenotype.
However, an important thing to keep in mind when considering family studies is the age of disease onset.
“For example, if your patient has a later onset disease that manifests later in life, say, in 40s or 50s, it is not useful in that situation to test young family members, unless they are showing signs of the disease. The laboratory can identify the VUS in those young family members, but they may be too young to say if they will develop the phenotype. In these situations, testing younger family members will not provide any evidence for reclassification,” Schleit described.
For some cases, not enough information may be known about the gene itself. “Genes of uncertain significance need even more evidence to demonstrate a disease gene association. This can come from additional families or from functional studies, etc.,” Schleit continued but emphasized that in many cases, reclassification is just not possible yet.
“Sometimes, it might just be a matter of waiting. With time, new evidence may be discovered that supports reclassification.”
Concrete benefits of reclassification to the genetic community: “Transparency in reporting is extremely important”
For the knowledge to accumulate, it is important that academia, healthcare institutions and industry to work together and team up to get genetic data reported and functional studies completed. Schleit gives an example from the JPH2 gene. Variants in this gene were often classified as VUSs due to an insufficient understanding of the gene’s role in cardiac disease. A recent report describing segregation of JPH2 variants with hypertrophic cardiomyopathy in six families has now allowed variants to be re-classified from VUS to likely pathogenic and further, to pathogenic. 1
“In the study by Vanninen et al., the collaboration between patient care, research and the diagnostic laboratory allowed for an in-depth analysis of the clinical history of the patients and their families to be combined with their genetic testing results.”
To conclude, Schleit felt that transparency in reporting is extremely important to allow reclassification.
“Labs must provide detailed interpretations outlining all evidence that was used to classify any variant(s) reported, or technical limitations that might be included in the testing. That way, it is easier to keep an eye out for new relevant publications for the variant or gene, or even contact a researcher studying that gene or disorder,” Schleit said.
If lucky, such collaboration could lead to further, clinically impactful studies.
- Heterozygous junctophilin-2 (JPH2) p.(Thr161Lys) is a monogenic cause for HCM with heart failure Vanninen SUM, Leivo K, Seppälä EH, Aalto-Setälä K, Pitkänen O, et al. (2018) Heterozygous junctophilin-2 (JPH2) p.(Thr161Lys) is a monogenic cause for HCM with heart failure. PLOS ONE 13(9): e0203422. https://doi.org/10.1371/journal.pone.0203422