VUS: Variant of Uncertain Significance. What does it mean?
VUS (sometimes written as VOUS) stands for Variant of Uncertain Significance. A VUS is a genetic variant that, based on the available evidence, cannot be clearly classified as either benign or pathogenic. This term is commonly used in clinical diagnostics when genetic testing is performed in affected patients.
A VUS is often considered a variant with potential pathogenic relevance because (1) it has a very low allele frequency across populations, (2) it occurs in a gene where other mutations have been reported as pathogenic for a disorder similar to that observed in the patient, and (3) its biological characteristics may suggest a possible functional impact on the activity of the protein encoded by the gene where the variant occurs. For example, in silico predictions may indicate a damaging effect on protein structure; the variant may lie close to exon–intron junctions and therefore potentially affect splicing; or it may occur at the same codon or nucleotide position where another pathogenic variant has already been described.
Why do VUSes exist?
When sequencing the human genome, millions of variants are detected in every individual.
Most are harmless differences between people.
Only a very small fraction cause disease.
The challenge of genomic medicine is not finding variants.
It is understanding which ones matter.
When does a variant become pathogenic?
Identifying a genetic variant is only the first step.
The real question is whether that variant is responsible for the patient’s condition.
In clinical genomics, variant classification relies on multiple types of evidence. These may include population frequency, segregation within the family, functional studies, previously reported cases, and computational predictions about the impact of the variant on the gene or the encoded protein.
In many situations, however, the available evidence is incomplete. A variant may be rare but never previously observed in affected individuals. Functional data may be missing. Family information may be unavailable. As a result, the variant cannot be confidently classified as either pathogenic or benign.
When this happens, the variant is classified as a Variant of Uncertain Significance (VUS).
How long does it take for a VUS to be reclassified?
In most cases, the classification of a Variant of Uncertain Significance does not change quickly.
Reclassification depends on the accumulation of new scientific and clinical evidence. This may include additional patients carrying the same variant, segregation data within families, functional studies, or improvements in population and disease databases. Because this evidence takes time to emerge, the interval before a VUS is reclassified can vary widely.
In clinical practice, when the results of Whole Exome Sequencing (WES) or Whole Genome Sequencing (WGS) remain inconclusive, it is often recommended to wait approximately 18 to 24 months before performing a systematic reanalysis of the genomic data. This reanalysis includes, among other aspects, the reassessment of previously reported variants, including significant VUS described in the original report.
From our experience as a diagnostic laboratory, a structured reanalysis performed after about two years may lead to the reclassification of roughly 10–20% of the variants originally reported. This includes variants initially reported as pathogenic in the context of carrier status for recessive conditions, as well as variants of uncertain significance potentially related to the patient’s phenotype.
In rare cases, new evidence deposited in the scientific literature may also lead to the reclassification of a previously reported VUS as likely benign. In our experience, such situations have been uncommon, but they illustrate how variant interpretation can evolve as genomic knowledge expands.
For this reason, the interpretation of a VUS should always be considered dynamic and evidence-dependent, rather than definitive at the time of the initial report. The clinical relevance of a variant can only be properly assessed within the broader context of the patient’s phenotype, family history, and diagnostic evaluation.
What does a VUS mean for the patient?
Receiving a Variant of Uncertain Significance can be confusing for patients and clinicians alike. Unlike pathogenic variants, a VUS does not provide a definitive explanation for the patient’s condition. At the same time, it cannot be dismissed as irrelevant.
In practical terms, a VUS represents a point where the available scientific evidence is not yet sufficient to determine whether the variant contributes to disease. The variant may eventually prove to be pathogenic as new cases are reported and additional data become available. In other situations, it may later be reclassified as benign.
For this reason, a VUS should not be interpreted as a diagnosis. Rather, it reflects the current limits of medical knowledge and the complexity of interpreting genetic variation in the human genome.
When a Variant of Uncertain Significance remains unresolved, the diagnostic process may require a broader clinical interpretation.
Why do we care about VUS?
Variants of Uncertain Significance represent a substantial proportion of the results reported in genetic testing. This is particularly true when large multigene panels, whole-exome sequencing, or whole-genome sequencing are performed, where the number of detected VUS can be considerable.
In affected patients in whom a clearly pathogenic variant cannot be identified, several VUS may emerge as potential candidate variants contributing to the disease.
Each VUS is therefore evaluated for its possible relevance to the patient’s phenotype based on several factors, including:
(1) the genotype (for example, whether the variant is present in a heterozygous or homozygous state),
(2) the mutational spectrum of the gene involved (that is, whether variants of a similar biological type have previously been reported as pathogenic in that gene), and
(3) the relevance of the gene to the clinical presentation of the patient.
At the same time, the expertise of a clinical genomics laboratory does not lie in reporting every possible VUS that may be detected. In many cases, the real challenge is the opposite: identifying which variants are truly relevant and which ones should remain in the background of the analysis.
In other words, expert interpretation often works by subtraction.
The goal is not to produce a long list of uncertain findings, but to focus attention on the variants that may actually explain the patient’s condition.
How can the clinical significance of a VUS be clarified?
In some situations, additional evidence can help clarify the significance of a Variant of Uncertain Significance and shift its interpretation toward a more definitive classification. In rare disorders, two main approaches are commonly used.
(1) Familial segregation studies.
The variant can be tested in family members (usually by targeted analysis such as Sanger sequencing) to determine whether it arose de novo in the affected individual, which is often considered strong evidence of pathogenicity in sporadic disorders. Alternatively, segregation analysis may show that the variant is present only in affected family members and absent in unaffected relatives, providing additional support for a pathogenic role.
(2) Functional in-vitro studies.
Functional assays can sometimes be used to evaluate the biological impact of a variant. This approach is often complex, as experimental systems must be specifically designed and validated for the variant under investigation. Nevertheless, functional studies may represent the only available strategy in certain situations—for example when additional affected family members are not available for segregation analysis, or when assessing the potential effect of deep intronic variants on RNA splicing.
VUS and preconception screenings
A common misconception concerns the perceived power of high-throughput sequencing (such as whole-exome sequencing or whole-genome sequencing) in preconception screening. Some people believe that performing whole-exome or whole-genome sequencing before having a child can eliminate the risk of genetic disease. This is not the case, and one of the reasons lies in the presence of Variants of Uncertain Significance (VUS).
Every individual is a healthy carrier of several genetic variants associated with recessive disorders. These conditions are typically inherited in an autosomal recessive or X-linked recessive manner—that is, they may occur in a child when both parents carry a pathogenic variant in the same gene, or when a mother carries a pathogenic variant in an X-linked gene that can affect male offspring.
Because many pathogenic variants associated with rare diseases have already been described in the scientific literature, targeted or high-throughput preconception screening can identify known disease-causing mutations and allow estimation of reproductive risk for those specific variants. However, every individual also carries additional rare variants whose clinical significance is unknown. These variants, classified as VUS, cannot be interpreted as pathogenic or benign at the time of testing.
In addition, the overall reproductive risk in the general population—currently estimated at around 3% (meaning that roughly three out of every one hundred pregnancies result in the birth of a child affected by a severe congenital disorder)—can only be partially reduced by any type of preconception screening in the parents. This is not only because of the presence of VUS, but also because of de novo mutations, that is, genetic variants that arise for the first time in the embryo and are not inherited from either parent. In populations with low levels of consanguinity, such as most Western populations, these de novo mutations represent one of the major causes of genetic disorders at birth.
That said, it is important to emphasize that couples who wish to explore even a fraction of their reproductive risk should have the opportunity to do so. Avoiding preconception screening simply because of the existence of VUS or de novo mutations would mean removing options from patients—and limiting options is itself a deliberate clinical choice.
Some genetic results cannot be interpreted automatically.
They require clinical reasoning and responsibility.