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Variant of uncertain significance

A variant of uncertain significance (VUS) is a genetic alteration identified through sequencing that cannot be reliably classified as either pathogenic or benign due to insufficient or conflicting evidence regarding its impact on disease risk or phenotype.^[1] In clinical genetics, VUS results are common, comprising up to 30-40% of findings in tests for hereditary conditions like cancer predisposition or cardiovascular disorders, as they often involve rare variants lacking robust population frequency data, functional assays, or segregation studies.^[2] The American College of Medical Genetics and Genomics (ACMG) and Association for Molecular Pathology (AMP) established standardized five-tier classification criteria in 2015—pathogenic, likely pathogenic, VUS, likely benign, and benign—based on weighted evidence from categories such as population genetics, computational predictions, biochemical function, and familial data; a VUS is assigned when criteria for pathogenic and benign categories balance or fail to meet thresholds.^[1] These guidelines emphasize that VUS should not influence clinical decision-making, as they do not confirm or exclude disease causation, and laboratories must report them with caveats urging periodic re-evaluation as new evidence emerges from databases like ClinVar or ongoing research.^[1] Challenges with VUS include patient anxiety from ambiguous results, potential over- or under-interpretation in multigene panels, and the need for follow-up strategies like family segregation testing or functional validation, which can reclassify approximately 7% of VUS over time.^[2] Efforts to refine VUS handling include proposals for subcategorization by pathogenicity probability (e.g., low, medium, high) to better guide counseling, though current ACMG standards prioritize caution to avoid misuse in medical management.^[3]

Background and Definition

Genetic Variants in Genomics

Genetic variants refer to alterations in the DNA sequence compared to a reference genome, encompassing a range of changes that can influence biological function. Common types include single nucleotide variants (SNVs), which involve the substitution of one nucleotide for another at a specific position; insertions/deletions (indels), which add or remove short stretches of nucleotides, typically up to 50 base pairs; and copy number variants (CNVs), which are larger structural changes involving the duplication or deletion of segments of DNA, often spanning thousands of base pairs or more.^[4]^[5]^[6] The advent of next-generation sequencing (NGS) technologies has profoundly transformed variant detection by enabling the rapid, cost-effective sequencing of entire genomes or targeted regions like exomes, uncovering millions of variants per individual that were previously undetectable with traditional methods. This surge in data generation—often producing billions of reads per sample—has expanded genomic testing in clinical and research settings but introduced significant interpretive challenges, as distinguishing disease-causing variants from neutral ones requires integrating diverse evidence like population frequency, functional impact, and segregation data.^[7]^[8] Assessing the clinical significance of genetic variants is crucial for diagnosing hereditary diseases, where pathogenic variants in single genes can explain Mendelian disorders like cystic fibrosis or Huntington's disease, guiding family counseling and targeted therapies. In cancer predisposition, germline variants in genes such as BRCA1 or BRCA2 identify individuals at elevated risk for tumors like breast or ovarian cancer, informing preventive strategies like enhanced screening or prophylactic surgery. Similarly, in pharmacogenomics, variants in genes like CYP2D6 or TPMT predict drug metabolism rates, optimizing dosing to minimize adverse reactions and improve efficacy for treatments in oncology, cardiology, and beyond.^[9]^[10]^[11] On average, a typical human genome harbors approximately 4-5 million SNVs and 600,000-1 million short indels relative to the reference sequence (as of 2023), alongside thousands of structural variants including CNVs, with the vast majority being benign polymorphisms that do not affect health. These variants are classified using frameworks like the five-tier system to determine their pathogenicity.^[4]^[12]

Defining a Variant of Uncertain Significance

A variant of uncertain significance (VUS) is a genetic alteration identified through sequencing whose association with disease cannot be definitively determined due to insufficient or conflicting evidence to classify it as benign, likely benign, likely pathogenic, or pathogenic.^[13] This classification applies when available data, such as population frequency, functional assays, or segregation studies, do not meet the thresholds required for more definitive categories under standardized guidelines.^[13] As a result, VUS results are not used to inform clinical decision-making, emphasizing the need for ongoing research to resolve their status over time.^[13] Key characteristics of VUS include a lack of reliable population frequency data indicating rarity in healthy individuals, ambiguous predictions of functional impact from in silico tools, or mixed results from limited experimental studies assessing protein function or cellular effects.^[1] For instance, a variant might show moderate evidence of altering splicing but lack corroborative data from patient cohorts or animal models, leading to its uncertain designation.^[1] These features highlight the provisional nature of VUS, distinguishing them from variants with clear supportive or refuting evidence. VUS are particularly prevalent in genes associated with hereditary cancers, such as BRCA1 and BRCA2, where historically 5–10% of individuals undergoing testing for hereditary breast and ovarian cancer risk received such results (as of the early 2010s); recent studies report rates around 2-6%, varying by population ancestry, with higher rates in non-European groups as of 2025.^[14]^[15] In these contexts, the variants often involve missense changes or intronic alterations whose disease relevance remains unclear without additional familial or functional data.^[16] The terminology has evolved from "variant of unknown significance" to "uncertain significance" to better reflect that some evidence typically exists, though it is inadequate for classification, rather than implying a complete absence of information.^[1] This shift, recommended in joint consensus guidelines, promotes precision in communicating the interpretive challenges to clinicians and patients.^[1]

Historical Development

Pre-2015 Classification Approaches

Prior to the establishment of standardized guidelines, the classification of genetic variants in the 1990s and early 2000s depended on ad hoc approaches, primarily involving family segregation analyses to assess co-inheritance with disease and basic bioinformatics tools for predicting functional impacts. These methods were applied inconsistently across laboratories, often without unified criteria, leading to subjective interpretations based on limited evidence such as evolutionary conservation or in silico predictions.^[17] In the context of hereditary cancer genes like BRCA1 and BRCA2, variants whose pathogenicity could not be clearly established were commonly labeled as "unclassified variants" (UVs), with laboratories employing informal scales to differentiate benign polymorphisms from potentially deleterious mutations. For instance, early BRCA testing protocols categorized variants based on rough assessments of rarity in population databases and preliminary functional data, but lacked rigorous thresholds, resulting in variable reporting practices. The American College of Medical Genetics (ACMG) attempted to provide initial structure through 2000 recommendations for sequence variant interpretation, emphasizing the need for multiple lines of evidence but stopping short of a tiered system. Early collaborative databases like ClinVar, launched in 2013, began facilitating data sharing to address these inconsistencies.^[18]^[19]^[20] These pre-standardization efforts were plagued by high inter-laboratory discordance, particularly for ambiguous variants, with studies reporting disagreement rates of approximately 27% in BRCA1 and BRCA2 classifications across multiple testing centers. Such inconsistencies arose from differing weightings of evidence types, like segregation data versus computational predictions, and contributed to clinical uncertainty in patient management. To mitigate these challenges, collaborative initiatives emerged, including the formation of the Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) consortium in 2009, which focused on pooling data and developing gene-specific algorithms for BRCA variant assessment through shared multifactorial likelihood models by 2010.^[21]^[22]

ACMG/AMP Guidelines and Evolution

The 2015 American College of Medical Genetics and Genomics (ACMG) and Association for Molecular Pathology (AMP) guidelines established a standardized framework for interpreting sequence variants, including variants of uncertain significance (VUS), by defining 28 evidence-based criteria categorized into population data (e.g., allele frequency), computational predictions, functional studies, and familial/segregation or clinical data.^[13] These criteria use a point system assigning weights—very strong, strong, moderate, supporting, or stand-alone—to support classifications across a five-tier system: pathogenic, likely pathogenic, VUS, likely benign, and benign.^[23] The framework aimed to reduce subjectivity in variant interpretation compared to pre-2015 ad hoc methods, emphasizing multidisciplinary evidence integration for consistent clinical reporting.^[24] Subsequent evolutions refined the guidelines for broader applicability. In 2018, ACMG updated recommendations for reporting secondary findings from clinical exome and genome sequencing, specifying conditions under which VUS in actionable genes should be disclosed or withheld to balance patient autonomy and clinical utility. By 2020, the Clinical Genome Resource (ClinGen) introduced gene- and disease-specific refinements through Variant Curation Expert Panels (VCEPs), adapting criteria weights and thresholds for genes like those in RASopathies or hearing loss to account for locus-specific variant effects and improve classification accuracy.^[25] Further updates in 2023 addressed criteria PP1 (segregation in families) and PP4 (phenotype specificity), providing quantitative Bayesian methods and thresholds for co-segregation data to strengthen evidence when family studies are limited, as detailed in ClinGen's SVI working group guidance.^[26] These refinements continued into 2024–2025, with applications in genes like FBN1 and tumor suppressors demonstrating enhanced reclassification of VUS using updated PP1/PP4 combinations.^[27]^[28] The guidelines' implementation has notably contributed to more consistent variant classifications and some reduction in VUS rates in clinical testing, though challenges persist; VUS remain common in novel or rare variants due to incomplete evidence.^[24] The 2015 ACMG/AMP guidelines reinforce that VUS should not inform clinical decisions, such as treatment or screening, echoing core principles from the original framework while addressing emerging genomic testing contexts.^[1]

Variant Classification Framework

Overview of the Five-Tier System

The five-tier classification system for genetic variants, developed by the American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP), categorizes sequence variants based on their predicted impact on disease. The tiers include pathogenic, which denotes variants that cause disease; likely pathogenic, defined as variants with greater than 90% probability of pathogenicity; variant of uncertain significance (VUS), indicating insufficient evidence to assign to another category; likely benign, encompassing variants with less than 10% probability of pathogenicity; and benign, referring to variants with no expected clinical impact. This system standardizes variant interpretation across clinical laboratories, enabling consistent reporting that informs medical decision-making, such as whether to pursue further testing or alter patient management. The classification relies on a Bayesian-like framework where evidence criteria are weighted by strength—such as very strong, strong, moderate, or supporting—and combined to meet predefined thresholds for each tier; for instance, a variant is deemed pathogenic if the cumulative evidence exceeds a 99% posterior probability of pathogenicity. The framework has achieved widespread global adoption, with endorsements and adaptations by organizations including the AMP as a co-developer, the Clinical Genome Resource (ClinGen) through ongoing specifications and updates, and the UK's Association for Clinical Genomic Science (ACGS) in its 2024 best practice guidelines for rare disease diagnostics.^[25]^[29]

Pathogenic and Likely Pathogenic Categories

In the ACMG/AMP five-tier variant classification system, the pathogenic and likely pathogenic categories designate germline sequence variants with high-confidence evidence of causality for a Mendelian disorder, enabling direct clinical application. Pathogenic variants meet stringent criteria indicating a clear disease-causing role, while likely pathogenic variants require moderate but compelling evidence, distinguishing both from variants lacking sufficient substantiation. Pathogenic classification requires one or more very strong pathogenic criteria, such as PVS1 for null variants (e.g., nonsense, frameshift, canonical splice site disruptions, or initiation codon variants) in genes where loss-of-function is an established disease mechanism, combined with at least one strong (PS1–PS4), two moderate (PM1–PM6), or equivalent supporting evidence (PP1–PP5). Alternatively, two or more strong criteria alone suffice, or one strong plus multiple moderate/supporting criteria. Strong criteria include PS2 for de novo variants (with maternity/paternity confirmation) in a proband with the disorder and no family history, or PS3 for well-established functional studies demonstrating a damaging effect. A representative example is a frameshift variant in TP53, such as c.645del (p.Ser215Argfs*32), which qualifies as pathogenic under PVS1 for Li-Fraumeni syndrome due to loss-of-function in this tumor suppressor gene.^[30]^[31] Likely pathogenic classification applies when evidence is robust but falls short of pathogenic thresholds, such as one very strong criterion (e.g., PVS1) plus one moderate, or one strong plus one to two moderate/supporting criteria. Moderate criteria encompass PM2 for variants absent or ultra-rare in population databases (e.g., gnomAD), or PM3 for variants in trans with a pathogenic allele in autosomal recessive disorders (verified by parental testing). Supporting evidence might include PP1 for cosegregation with disease in a small family or PP3 for multiple in silico predictions of deleteriousness. For instance, a missense variant predicted deleterious by computational tools and segregating in a limited affected pedigree could meet likely pathogenic status if aligned with gene-specific context. These classifications carry substantial clinical weight, directly supporting diagnosis, risk assessment, and targeted interventions such as enhanced cancer screening protocols in Li-Fraumeni syndrome or carrier testing in recessive conditions.^[30] Unlike variants of uncertain significance, pathogenic and likely pathogenic designations justify medical actions, including family cascade screening and personalized management plans.

Benign and Likely Benign Categories

In the ACMG/AMP variant classification framework, the Benign category is assigned to genetic variants that exhibit strong evidence of having no disease-causing effect, serving as the counterpart to the Pathogenic category by confirming non-contributory status.^[13] A key stand-alone criterion for Benign classification is BA1, which applies when the variant's allele frequency exceeds 5% in population databases such as the Exome Aggregation Consortium (ExAC), 1000 Genomes Project, or Exome Sequencing Project (ESP), indicating it is a common polymorphism unlikely to cause rare disorders.^[13] Additional supporting criteria include BS3, where well-established functional studies demonstrate no damaging effect on the gene or protein product, and BP7, applicable to synonymous variants that do not alter the amino acid sequence and lack predicted impacts on splicing.^[13] Classification as Benign requires either the BA1 criterion alone or a combination of at least one strong benign criterion (BS1–BS4) and one supporting benign criterion (BP1–BP7), ensuring robust evidence against pathogenicity.^[13] The Likely Benign category captures variants with moderate evidence supporting a non-disease-causing role, distinguishing them from variants of uncertain significance (VUS) by meeting defined thresholds that fall short of full Benign status but still favor harmlessness.^[13] For instance, BS1 supports Likely Benign when the allele frequency is greater than expected for the disorder's prevalence (e.g., >0.5% for ultra-rare conditions, per Table 6 in the guidelines) but does not reach the 5% threshold for BA1.^[13] Similarly, BP4 provides supporting evidence if multiple computational tools predict no impact on protein function or splicing, often applied to missense or in-frame variants tolerated by predictive models.^[13] To achieve Likely Benign, evidence must include at least one strong benign criterion or a combination such as one strong and multiple supporting criteria (e.g., BS1 plus two or more BP criteria), preventing overclassification as VUS when benign signals predominate.^[13] Representative examples of Benign and Likely Benign variants include common polymorphisms in non-coding regions, such as intronic single nucleotide variants (SNVs) with high minor allele frequencies (>5%) that show no association with altered gene expression or splicing in population studies.^[13] These classifications play a crucial role in variant filtering during genomic analysis pipelines, where Benign and Likely Benign calls are systematically excluded from prioritization lists to focus computational and clinical resources on potential true positives, thereby enhancing the efficiency of identifying disease-relevant variants.^[13]

Uncertain Significance Category

A variant of uncertain significance (VUS) is classified as such when there is insufficient or conflicting evidence to determine whether it is pathogenic or benign, often involving novel or rare sequence changes that do not meet the strength thresholds for other categories in the five-tier system. These variants typically exhibit mixed predictions from in silico tools, such as conflicting results from predictors like SIFT or PolyPhen-2, and lack robust supporting data from population frequencies, functional studies, or segregation analyses. Unlike pathogenic variants, which accumulate strong evidence of disease causality, or benign variants backed by high population allele frequencies, VUS remain in interpretive limbo due to evidential gaps, making them particularly common among missense alterations in understudied genomic regions.^[13] The prevalence of VUS in clinical genetic testing reports ranges from 10% to 40%, depending on the gene panel, disease context, and testing population, with higher rates observed in diverse non-European ancestry groups due to underrepresentation in reference databases like gnomAD. For instance, in hereditary cancer syndrome testing, VUS constitute up to 41% of findings in large cohorts, predominantly missense variants that evade clear classification. This elevated frequency in underrepresented populations underscores the challenge of applying evidence criteria calibrated primarily on European-descent data, leading to a disproportionate burden of uncertainty in global genomic medicine.^[32]^[2]^[33] While the standard ACMG/AMP framework does not endorse formal subclasses for VUS, some clinical laboratories employ internal tiering, such as "leaning pathogenic" or "likely VUS," to convey nuanced evidential balances without altering the core classification; however, these are not universally adopted and risk introducing inconsistency across reports. Reporting standards for VUS emphasize transparency, requiring documentation of all evaluated evidence and, where applicable, confidence intervals for allele frequency estimates from population databases to contextualize rarity without implying benignity. This approach ensures that VUS reports facilitate future reclassification as new data emerge, prioritizing reproducibility over speculative gradations.^[34]^[13]

Assessment Methods for VUS

Evidence Types and Criteria

The American College of Medical Genetics and Genomics (ACMG) and Association for Molecular Pathology (AMP) guidelines establish a structured framework for evaluating variants of uncertain significance (VUS) through specific evidence categories, each weighted as very strong, strong, moderate, or supporting for pathogenicity or benignity.^[35] These categories integrate diverse data types to assess whether a variant's impact can be resolved, with VUS classification applied when evidence is insufficient or conflicting to assign a more definitive tier.^[35] The framework emphasizes combining multiple lines of evidence, as no single category is typically decisive for reclassification.^[35] Population data provide critical context for variant rarity and allele frequency, informing benign or pathogenic interpretations. The PVS1 criterion applies as very strong evidence of pathogenicity for predicted null variants (e.g., nonsense, frameshift, canonical splice site disruptions) in genes where loss-of-function is a known disease mechanism, provided the variant is expected to undergo nonsense-mediated decay or disrupt protein function.^[35] Conversely, BS1 offers strong benign evidence when a variant's allele frequency in population databases exceeds the expected prevalence for the disorder in question, such as frequencies above 0.005 for rare recessive conditions.^[35] Additional population metrics, like BA1 for common alleles (>5% frequency) or PM2 for extremely rare variants (<0.0001 in controls), further refine VUS assessments by highlighting deviations from population norms.^[35] Computational predictions evaluate a variant's potential functional impact based on sequence conservation, physicochemical properties, and evolutionary models. The PP3 criterion serves as supporting pathogenic evidence when multiple in silico tools predict a deleterious effect, such as those assessing missense changes for disruption of protein structure or interactions.^[35] Tools like SIFT and PolyPhen-2 exemplify this approach, flagging variants as damaging if they alter conserved residues in functional domains.^[35] In contrast, BP4 provides supporting benign evidence for predictions of tolerance or neutrality across similar tools, indicating the variant is unlikely to impair protein function.^[35] These predictions are weighted modestly due to their indirect nature and variable accuracy across gene contexts. Functional studies directly test a variant's biological effect, offering robust evidence for VUS resolution. The PS3 criterion awards strong pathogenic evidence for well-established in vitro or in vivo assays demonstrating loss-of-function or damaging gain-of-function, such as reduced enzyme activity, impaired protein localization, or altered cellular phenotypes in model systems.^[35] For instance, assays showing <10% residual activity compared to wild-type can support reclassification if corroborated by gene-specific knowledge.^[35] Benign counterparts, like BS3 for assays confirming normal function, similarly aid in downgrading VUS, though such studies require rigorous controls and replication to avoid overinterpretation.^[35] Familial and segregation data assess inheritance patterns and co-occurrence with disease phenotypes in pedigrees. The PS4 criterion provides strong pathogenic evidence when the variant is identified in multiple unrelated individuals with the phenotype, with strength scaled by case numbers (e.g., ≥3 unrelated cases for very strong).^[35] PP1 offers supporting evidence for co-segregation with disease in multiple affected family members, upgraded if observed in >8 meioses without recombination.^[35] De novo occurrences (PS2, strong) or assumed de novo (PM6, moderate) in affected probands further bolster pathogenicity, particularly for dominant disorders with high penetrance.^[35] Lack of segregation (BS4, strong benign) in large families can conversely support benign classification. Clinical data, including structural impacts and phenotypic associations, contribute moderate to supporting evidence. The PM4 criterion applies moderate pathogenic evidence to protein length changes, such as in-frame deletions/insertions in non-repeat regions that disrupt critical domains without abolishing the protein entirely.^[35] For example, disruptions to functionally important motifs like active sites qualify if the variant is not observed in controls.^[35] Related criteria, such as PM3 for variants in trans with known pathologics in affected individuals (moderate, upgraded per occurrence), integrate patient-specific observations to contextualize VUS within disease models.^[35] These elements ensure clinical relevance while requiring gene- and disorder-specific calibration for accurate application.

Computational Tools and Functional Assays

Computational tools, particularly in silico predictors, play a key role in assessing variants of uncertain significance (VUS) by estimating their potential pathogenicity based on sequence conservation, biochemical properties, and evolutionary constraints. Tools such as Combined Annotation Dependent Depletion (CADD) integrate multiple annotations to produce a phred-scaled score that ranks variants relative to simulated deleterious changes, aiding in the prioritization of VUS for further investigation. Similarly, the Rare Exome Variant Ensemble Learner (REVEL) employs a machine learning ensemble of 18 predictors to achieve higher accuracy in distinguishing pathogenic from benign missense variants, outperforming individual tools in benchmarks. However, these in silico methods have limitations, with predictive accuracies typically ranging from 60% to 80% across diverse datasets, often leading to false positives or negatives that require corroboration with other evidence types.^[36]^[37] Functional assays provide direct experimental evidence for VUS by evaluating their impact on protein function, splicing, or organismal phenotypes, often supporting the ACMG/AMP PP3 (pathogenic) or BP4 (benign) computational criteria. In vitro assays, such as minigene splicing tests, insert the variant into a reporter construct to assess alterations in RNA processing; for instance, these have reclassified VUS in genes like USH2A by demonstrating aberrant splicing patterns. In vivo models, including zebrafish knockdown or overexpression for cardiac-related genes, reveal phenotypic effects like heart malformations, offering organism-level insights but at the expense of longer timelines. These assays are resource-intensive, with costs often exceeding thousands of dollars per variant and requiring weeks to months for completion, limiting their routine use.^[38]^[39]^[40] Recent advancements in multiplexed assays of variant effect (MAVE) enable high-throughput functional testing of thousands of variants simultaneously, addressing the scalability issues of traditional assays. MAVEs, such as those using saturation genome editing in cell lines, quantify variant effects on fitness or expression, with 2024 guidelines standardizing reporting to improve clinical integration. The MaveDB database, updated in 2024, curates over seven million variant effect measurements from more than 100 studies, facilitating reuse for VUS resolution. Databases like ClinVar aggregate expert-curated classifications and functional data submissions, allowing VUS to be tracked and re-evaluated as new evidence emerges, while gnomAD provides population allele frequencies to infer benign status if variants exceed rarity thresholds for the gene.^[41]^[42]^[43]^[44]

Challenges and Limitations

Classification Subjectivity and Variability

The classification of variants of uncertain significance (VUS) under the ACMG/AMP guidelines is inherently subjective due to the interpretive nature of weighting evidence categories, such as distinguishing between "moderate" and "supporting" levels of pathogenicity or benignity. For instance, criteria like PS3 (functional studies) or PM4 (protein length changes) require evaluators to assess the strength of supporting data, where a moderate rating implies odds of pathogenicity around 4:1, compared to supporting at 2:1, leading to variable point assignments across classifiers. This subjectivity arises from differences in how laboratories prioritize qualitative aspects of evidence, such as the relevance of computational predictions or population frequency data, often resulting in borderline decisions that default to VUS. Additionally, cultural and population biases in reference databases exacerbate this, as variants in underrepresented ancestries are less likely to meet benign thresholds due to limited allele frequency data from diverse populations.^[24]^[13]^[45] Inter-laboratory variability in VUS classification has been well-documented, with studies prior to 2020 reporting discordance rates of 20-40% when comparing classifications across clinical labs, often involving shifts between VUS and likely benign or likely pathogenic categories. For example, a 2016 multicenter evaluation found only 34% concordance for VUS among labs applying early ACMG criteria, attributed to inconsistent application of evidence rules. Post-2015 guidelines, these rates improved to 10-15% for clinically significant discordances (e.g., pathogenic/likely pathogenic vs. VUS), as seen in a 2020 analysis of 155 variants where 11% showed impactful differences, largely resolved through standardized training and shared resources like ClinVar. However, overall conflicting interpretations remain around 40-50% in broader surveys, highlighting persistent challenges in harmonizing outputs.^[46]^[47]^[48] Contributing factors to this variability include laboratory experience, with less specialized centers showing higher rates of VUS assignment due to cautious interpretations, and gene-specific knowledge gaps that amplify uncertainty in understudied loci. Notably, individuals of non-European ancestry face disproportionately higher VUS rates—up to 20-30% more than European-descent cohorts—stemming from ancestry-biased databases that underrepresent non-European variants, leading to insufficient evidence for reclassification. In response, the 2025 ACMG/ClinGen recommendations emphasize the use of expert consensus panels, such as those coordinated by the Sequence Variant Interpretation Working Group, to review discordant cases and promote uniform application of criteria through iterative specifications and training modules. These panels aim to reduce subjectivity by fostering collaborative evidence review, particularly for ancestry-diverse variants.^[2]^[49]^[25]

Reclassification Processes and Rates

Reclassification of variants of uncertain significance (VUS) occurs through systematic, periodic reviews by genetic testing laboratories and clinical teams, incorporating emerging evidence to refine classifications under the American College of Medical Genetics and Genomics (ACMG) and Association for Molecular Pathology (AMP) framework. This process often involves resubmitting variants to public repositories like ClinVar, where cumulative submissions from multiple laboratories provide population-level data, in silico predictions, and functional assay results to support reinterpretation. Laboratories typically outline recontact policies in informed consent documents, directing notifications to ordering clinicians rather than patients directly, who then relay updates to affected individuals, though implementation varies by institution and jurisdiction.^[50]^[51]^[52] Reclassification rates for VUS generally range from 5% to 30% over 2 to 8 years, with the majority shifting to benign or likely benign categories based on aggregated evidence. In hereditary disease testing cohorts, approximately 5.9% of VUS were reclassified over an 8.5-year period, predominantly to benign/likely benign (78.8% of changes). For BRCA1/2 genes in breast and ovarian cancer panels, rates are higher, with 30% to 41% of VUS downgraded to benign or likely benign within 5 years, reflecting gene-specific data accumulation.^[53]^[52]^[54] Triggers for reclassification include updates to population databases like gnomAD and ClinVar, novel functional studies such as RNA splicing assays, and family segregation analyses. The 2025 ClinGen refinements to ACMG criteria PP1 (co-segregation) and PP4 (phenotype specificity) introduce a points-based system that better integrates locus homogeneity and diagnostic yield data, facilitating reclassification of about 30.7% of VUS in tumor suppressor genes like NF1 and FH by assigning scores up to 5 points for high-specificity phenotypes.^[55]^[52] The interim "pending" status of VUS often heightens patient anxiety and disrupts clinical decision-making, as individuals grapple with unresolved uncertainty. Ethical challenges encompass the professional duty to pursue recontact for actionable reclassifications, weighing benefits against risks of psychological distress, resource strain on healthcare systems, and potential inequities in follow-up for diverse populations.^[56]^[57]^[58]

Clinical Applications

Implications for Genetic Counseling

Genetic counselors play a crucial role in explaining variants of uncertain significance (VUS) to patients, emphasizing the inherent uncertainty without over-interpreting the results as either pathogenic or benign. This involves clearly communicating that a VUS indicates insufficient evidence to determine its clinical impact, thereby avoiding assumptions that could lead to inappropriate medical decisions.^[1] To enhance understanding, counselors often employ visual aids, such as diagrams illustrating probability spectrums or pie charts representing classification categories, which have been shown to improve comprehension of genetic concepts during sessions.^[59] Patients receiving VUS results commonly experience heightened anxiety and genetic test-specific concerns compared to those with negative findings, though less severe than with pathogenic variants, potentially leading to false reassurance if the uncertainty is not adequately addressed.^[56] Qualitative studies indicate varied reactions, including distress, frustration, and incomplete risk perception, with some patients seeking additional consultations or more frequent follow-ups to manage the ambiguity.^[56] These emotional responses underscore the need for tailored counseling to mitigate decisional regret. In family contexts, VUS findings limit cascade testing recommendations, as relatives should not undergo targeted testing for the variant due to its uncertain clinical relevance, preventing unnecessary anxiety or costs without actionable outcomes.^[60] Counselors may discuss family segregation patterns—such as whether the variant tracks with disease in relatives—but must refrain from drawing conclusions, instead framing it as exploratory data that could inform future re-evaluations without altering current management.^[61] Best practices in genetic counseling for VUS, as outlined in professional guidelines, include using standardized, scripted language in reports and sessions to consistently convey uncertainty, such as phrases emphasizing "insufficient evidence for classification" to promote clarity and reduce misinterpretation.^[62] The American College of Medical Genetics and Genomics (ACMG) recommends that VUS results not influence clinical decisions, guiding counselors to focus on emotional support and education while monitoring for reclassification opportunities through ongoing databases.^[1] Recent National Society of Genetic Counselors (NSGC) resources further advocate for orienting language that directs patient focus toward probabilistic understanding and family communication strategies.^[63]

Management in Patient Care

In clinical practice, variants of uncertain significance (VUS) are explicitly not used to guide medical management decisions, as they lack sufficient evidence to confirm pathogenicity or benignity. According to the American College of Medical Genetics and Genomics (ACMG) guidelines, clinical recommendations should instead rely on personal and family medical history, standard screening protocols, and other established risk factors. For instance, prophylactic surgeries such as mastectomy or oophorectomy are not recommended based on a VUS result alone, avoiding unnecessary interventions that could lead to harm.^[64]^[65]^[66] In cancer genetics, this approach means patients with VUS in genes like BRCA1 or BRCA2 continue with routine surveillance, such as mammograms or colonoscopies, tailored to their age, family history, and environmental risks rather than altering protocols due to the variant. Insurance providers often deny claims for enhanced screening or preventive measures justified solely by a VUS, reinforcing the non-actionable nature of these findings and preventing overutilization of resources. This conservative stance helps mitigate patient anxiety from inconclusive results while ensuring equitable access to evidence-based care.^[67]^[68] Ethical considerations in managing VUS emphasize robust informed consent processes prior to genetic testing, where patients are clearly apprised of the potential for uncertain results and their implications for decision-making. This is particularly critical given the higher prevalence of VUS among underrepresented racial and ethnic groups, such as Black, Hispanic, and Asian individuals, due to underrepresentation in genetic databases, which can exacerbate health disparities in access to definitive risk assessments. Addressing these equity issues requires ongoing efforts to diversify genomic data and tailor counseling to cultural contexts.^[69]^[70]^[71] Integration of VUS results into patient care often involves multidisciplinary teams, including geneticists, oncologists, and ethicists, to review cases holistically and recommend family history-based strategies. Recent 2025 ACMG updates, including gene-specific guidelines for variants in RAD51C, RAD51D, and BRIP1, further stress the non-actionable status of VUS, urging clinicians to prioritize reclassification efforts and avoid management changes until clearer evidence emerges. These teams facilitate coordinated care, such as periodic variant reassessment, to potentially resolve uncertainties over time.^[72]^[73]^[74]

Recent Advances and Future Outlook

Guideline Updates Post-2015

Following the foundational 2015 ACMG/AMP guidelines for variant interpretation, subsequent updates have refined approaches to variants of uncertain significance (VUS) through expert panel specifications and international harmonization. In 2020, the Clinical Genome Resource (ClinGen) advanced gene- and disease-specific modifications to the ACMG/AMP criteria via its Variant Curation Expert Panels (VCEPs), enabling tailored evidence weighting to address context-dependent variant impacts and reduce VUS rates. For hypertrophic cardiomyopathy, the Cardiomyopathy VCEP specified adjustments for sarcomeric genes such as MYH7 and MYBPC3, recalibrating criteria like PS3 (functional studies) and PP1 (segregation) to account for disease penetrance and phenotypic variability, which improved classification consistency across 60 tested variants.^[75] The 2023 specifications from the ENIGMA BRCA1/BRCA2 VCEP, approved by ClinGen, introduced enhanced splicing assessment rules (e.g., refined BP7 and PM2 applications for intronic variants), leading to reclassification of approximately 20-30% of BRCA1/2 VUS as benign through integration of in silico predictions, minigene assays, and population data. These updates prioritized splicing-altering variants, which constitute a significant portion of unresolved BRCA VUS, and were piloted on over 100 variants to validate their discriminatory power.^[76]^[52] As of November 2025, the ACMG/AMP is developing version 4.0 of the sequence variant classification standards in collaboration with ClinGen and CAP, focusing on standardized VUS reporting to clinicians and insurers by mandating disclosure of evidence strength and potential implications for risk assessment. This iteration adds subclasses like "VUS, favor benign" based on combined benign evidence (e.g., threshold-based BS4 for population frequency), aiming to guide insurance coverage and therapeutic decisions while maintaining the five-tier system.^[77] Aligning with global efforts, the 2023 Association for Clinical Genomic Science (ACGS) UK guidelines unified single nucleotide variant (SNV) and copy number variant (CNV) interpretation, incorporating CNV-specific evidence such as breakpoint analysis and allele frequency into ACMG/AMP codes (e.g., adapting PM2/BS2 for structural variants) to resolve VUS in rare diseases. This framework supports multinational data sharing and has been adopted by UK laboratories to harmonize with ClinGen and ENIGMA protocols.^[78]

Technologies for Resolving VUS

High-throughput functional genomics approaches, such as multiplexed assays of variant effect (MAVE) and CRISPR-based screens, enable the scalable assessment of thousands of genetic variants simultaneously to determine their functional impact. These methods introduce variants into cellular models and measure phenotypic outcomes, providing evidence to reclassify variants of uncertain significance (VUS). For instance, MAVE studies on the TP53 gene have integrated functional data from multiple assays, allowing for the reclassification of 69% of TP53 VUS as benign or pathogenic according to ClinGen specifications. Similarly, CRISPR-based deep mutagenesis screens, including those using prime editing, have resolved substantial proportions of VUS in genes like TP53 by linking variant genotypes to precise phenotypic effects in endogenous contexts.^[49]^[79] Artificial intelligence and machine learning models have advanced VUS resolution by predicting the pathogenicity of missense variants with high accuracy. The AlphaMissense model, developed using deep learning on protein structure and evolutionary data, classifies 89% of possible human missense variants as likely benign or likely pathogenic, achieving over 90% precision on ClinVar benchmarks. This represents a significant improvement over prior tools, increasing the fraction of confidently classified variants from 67.1% to 92.9% at 90% precision thresholds. Such models prioritize structural disruptions and evolutionary conservation, aiding in the prioritization of VUS for experimental validation.^[80]^[81] Integration of large-scale genomic databases like gnomAD version 4 (released in 2023 with updates in 2024) enhances VUS resolution by incorporating allele frequency data from diverse ancestries, including over 138,000 non-European individuals. This expanded representation reduces misclassification of benign variants in underrepresented populations, where VUS rates were previously higher due to limited reference data; studies using gnomAD v4 demonstrate decreased diagnostic uncertainty and improved equity in variant interpretation across ancestries. By providing population-specific frequencies, these resources support ACMG/AMP criteria for benign classifications, contributing to overall VUS reductions of 15-20% in diverse cohorts through better-powered statistical assessments.^[82]^[83] Analyses predict that by 2030, fewer than 10% of coding region VUS will remain unresolved, driven by synergies among functional assays, AI predictors, and population databases, though progress may vary by gene and ancestry. Ongoing clinical trials in pharmacogenomics are leveraging these technologies to test VUS resolution in drug response contexts, further accelerating reclassification rates.^[84]

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