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Challenges and Considerations in Sequence Variant Interpretation for Mendelian Disorders.

Young Eun Kim1, Chang Seok Ki2, Mi Ae Jang3

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|May 1, 2019
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Summary

The 2015 American College of Medical Genetics and Genomics (ACMG) guidelines for sequence variant interpretation, while widely adopted, can lead to inconsistencies. Ongoing efforts are needed to enhance the objectivity and reproducibility of variant classification in clinical practice.

Keywords:
American College of Medical Genetics (ACMG)Mendelian disorderVariant interpretation

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Area of Science:

  • Genetics
  • Molecular Biology
  • Clinical Diagnostics

Background:

  • The 2015 American College of Medical Genetics and Genomics (ACMG) and Association for Molecular Pathology (AMP) guidelines standardize sequence variant interpretation.
  • Despite standardization, subjectivity in guidelines can cause inconsistent variant classification across clinical laboratories.

Purpose of the Study:

  • To describe critical elements and potential pitfalls in sequence variant interpretation processes.
  • To provide updated information based on recent literature for Mendelian disorders.
  • To highlight the need for improved reproducibility and objectivity in variant classification.

Main Methods:

  • Review of recent literature on sequence variant interpretation.
  • Analysis of practical examples to illustrate interpretation processes and pitfalls.
  • Application of variant classification to Mendelian disorders.

Main Results:

  • Identified critical elements and potential pitfalls in current variant interpretation workflows.
  • Demonstrated how subjectivity can lead to inconsistent classification of variant pathogenicity.
  • Highlighted the broad applicability of interpretation methods across various genetic testing modalities.

Conclusions:

  • Standardized guidelines for sequence variant interpretation require ongoing refinement to minimize subjectivity.
  • Enhanced objectivity and reproducibility are crucial for accurate pathogenicity assessment of variants.
  • Continued efforts are necessary to improve consistency in variant classification across clinical laboratories globally.