Stepwise ABC System for Classification of Genetic Variants: Enhancing Clinical and Functional Insights

The classification of genetic variants has long been a cornerstone of precision medicine, providing essential insights for clinicians, researchers, and patients. In recent years, the American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) have led the way in developing widely accepted frameworks for variant classification. However, as the landscape of genomic research continues to evolve, so does the need for a more flexible, nuanced system that can adapt to a broader range of genetic data.

This blog post explores the Stepwise ABC System introduced in the European Journal of Human Genetics, which aims to refine and expand upon the existing ACMG classification framework. By separating the functional and clinical assessments of genetic variants, the ABC system offers a structured approach that enhances variant classification, particularly in complex genetic contexts.

Understanding the Limitations of the ACMG System
The ACMG-AMP system is a five-tiered framework that classifies genetic variants as benign, likely benign, variant of uncertain significance (VUS), likely pathogenic, or pathogenic. While this system has been instrumental in genetic testing, especially for high-penetrance dominant variants, it falls short in several areas. The system tends to merge clinical and functional data into a single dimension, making it less informative in cases where a variant's molecular function might not immediately translate into a clear clinical picture.

Moreover, the ACMG framework struggles with low-penetrance or recessive variants, where the relationship between genotype and phenotype is less straightforward. It also lacks precision when dealing with variants that don't fit neatly into a single disease phenotype, such as copy number variants (CNVs), hypomorphic alleles, and regulatory variants.

The Stepwise ABC System: A Two-Step Approach
The Stepwise ABC System aims to address these limitations by providing a two-step approach to genetic variant classification:
Step A: Functional Grading
Step B: Clinical Grading

In this model, variants are first evaluated based on their biological consequences (functional grading), and then their genotype-phenotype correlations (clinical grading). This separation ensures that the functional impact of a variant is assessed independently of its clinical significance, which can be highly variable depending on factors such as penetrance, environmental influences, and disease mechanisms.

Functional Grading: Prioritizing Biological Impact
In Step A, variants are classified purely based on their functional impact on gene or protein function. This grading system ranges from 0 (no functional effect) to 5 (proven functional effect), allowing researchers to clearly assess how a variant might disrupt gene function without prematurely linking it to clinical outcomes. This functional grading can also be applied to a wide range of genetic phenomena, such as enhancer variants, runs of homozygosity, and imprinted alleles.

One of the key innovations of the ABC system is the splitting of the VUS (class 3) category into two subgroups:
True unknowns (class 0): Cases where there is insufficient evidence to classify a variant.
Hypothetical functional effects (class 3): Variants that have some evidence of functional impact but do not yet meet the criteria for being classified as likely pathogenic.

This distinction helps avoid confusion, allowing clinicians to better understand when a variant might warrant further investigation.

Clinical Grading: Genotype-Phenotype Matching
Step B focuses on the clinical relevance of a variant by assessing its association with specific disease phenotypes. The clinical grading ranges from 0 (no conceivable genotype-phenotype correlation) to 5 (high-penetrance pathogenic variant). This step evaluates whether the variant aligns with known disease mechanisms or phenotypes, and it can be especially useful for identifying risk factors or variants of interest that may not directly cause disease but contribute to its development.

In this step, variants with clear biological effects but uncertain clinical consequences (e.g., a de novo variant that doesn’t fully match the patient’s phenotype) are separated from those with well-established clinical significance. This separation helps prioritize which variants should be flagged for further clinical follow-up or family screening.

Advantages of the ABC System
The Stepwise ABC System offers several advantages over traditional classification models:
Broader applicability: The ABC system can classify a wider range of genetic variants, including those involved in recessive diseases, low-penetrance conditions, and regulatory functions.

Improved clarity: By separating functional and clinical grading, the system provides clearer guidance to clinicians, reducing the risk of misinterpretation and enabling more informed decision-making.

Flexibility: The ABC system is compatible with existing ACMG classifications but can also function independently as an alternative framework, offering greater versatility in variant analysis.

Standardized reporting: The final classification combines both functional and clinical grades into a joint class (ranging from A to F), which is linked to standardized comments. These comments can be tailored to specific clinical questions, helping ensure that variant reports are relevant and actionable for healthcare providers.

Case Studies and Practical Applications
To illustrate its utility, the paper outlines several case studies where the ABC system was used to classify variants in a clinical setting. In one case, a BRCA2 variant was identified in a family with ovarian cancer. While the ACMG system classified this variant as "likely pathogenic" based on molecular evidence, the ABC system provided a more nuanced assessment by factoring in the variant’s clinical presentation. As a result, the variant was classified as a "susceptibility variant," providing more tailored guidance for patient management.

Similarly, in a case involving F5 Leiden, a well-known risk factor for venous thrombosis, the ABC system classified the variant based on its functional impact (disruption of gene function) and its clinical relevance (association with increased thrombosis risk), ensuring that the variant’s significance was accurately communicated to clinicians.

Conclusion: A Path Forward for Genetic Variant Classification
As precision medicine continues to grow, the need for more sophisticated tools to classify genetic variants is paramount. The Stepwise ABC System represents a significant step forward by providing a more flexible, transparent, and clinically relevant approach to variant classification. By separating functional and clinical assessments, this system helps clinicians and researchers make better-informed decisions, ultimately improving patient outcomes.

For laboratories and clinicians seeking a more comprehensive approach to variant interpretation, the ABC system offers a valuable alternative to the ACMG framework, ensuring that the complexity of genetic data is adequately captured and effectively communicated.

Reference:
Houge, G., Laner, A., Cirak, S., de Leeuw, N., Scheffer, H., & den Dunnen, J. T. (2022). Stepwise ABC system for classification of any type of genetic variant. European Journal of Human Genetics, 30(2), 150-159.