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Interpreting Genomic Variation: Fundamental Principles

Learn the principles and language of genomic variant interpretation and enhance your working knowledge of the ACMG guidelines.

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Discover the principles of genetic variant interpretation

Our individual genomes make us unique, and contribute to both rare and common disease.

In genomic testing, it’s vital to distinguish the clinically relevant, disease-causing variant from its background normal genomic variation in order to safely manage patients.

Get variant interpretation training for effectively managing patients

This course is designed to educate health professionals involved in the variant journey from the laboratory to the patient.

You’ll explore the fundamental principles of variant interpretation and review the American College of Clinical Genetics and Genomic (ACMG) and The Association for Clinical Genomic Science (AGCS) guidelines. You will also take a detailed look at the tools available to aid genomic variant interpretation.

Study the ACMG and ACGS guidelines in theory and practice

The ACMG and ACGS guidelines were developed to promote consistency in the tools used to classify a genomic variant as pathogenic, likely pathogenic, likely benign, benign, or uncertain.

You’ll explore how the ACMG evaluated each of the tools and applied a weighting, as well as the algorithm developed to combine the evidence from each of these tools.

You’ll be encouraged to apply your learning through workshopped examples that illustrate both the strengths and weaknesses of the ACMG tools and framework.

This course is part of a series with Interpreting Genomic Variation: Inherited Cancer Susceptibility.


  • Week 1

    Introduction to genomic variation and population data

    • Introduction to course

      In this first section, we welcome you to the course with more information about our course team and some key definitions.

    • Normal Genetic Variation

      In this section, we review and refresh our knowledge on normal genetic variation.

    • Changing technologies

      In this section, we examine the evolution of genomic testing technologies and the nomenclature used for genomic variation.

    • Variant classification

      In this section, we provide an introduction to how genomic variant classification affects patient care.

    • Tools for variant interpretation: Population databases

      In this section, we look at the first of our fundamental principles for genomic variant interpretation - population data.

  • Week 2

    Tools for genomic variant interpretation

    • Welcome to week 2

      In this section, we look ahead to what is to come in this week.

    • Tools for genomic variant interpretation: Computational and predictive data

      In this section, we examine how different types of variants may impact pathogenicity as well as the computational predictions available.

    • Tools for genomic variant interpretation: Functional data

      In this section, we explore the different types of functional data available.

    • Tools for genomic variant interpretation: Reputable databases

      In this section, we look at the range of reputable databases which can be useful for genomic variant interpretation.

    • Tools for variant interpretation: Phenotyping and literature searches

      In this section, we look at the importance of good phenotyping and literature searches.

    • Ethics of genomic variant interpretation

      In this section, we hear another patient's experience with VUS and consider the ethics of genomic variant interpretation.

  • Week 3

    Clinical genomic variant interpretation

    • Welcome to week 3

      In this section, we look ahead to what is to come in this final week.

    • ACMG & ACGS guidelines

      In this section, we go through the American College of Medical Genetics and Genomics (ACMG) guidelines for variant interpretation, as well as additional recommendations from the Association for Clinical Genomic Science (ACGS).

    • VUS multidisciplinary meetings

      In this section, we examine the role of multidisciplinary team (MDT) meetings in variant interpretation and the importance of good communication skills.

    • Genomic variant interpretation in practice

      In this final section of the course, you will have the opportunity to practice variant interpretation using the fundamental principles and guidelines we have covered.

When would you like to start?

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Learning on this course

On every step of the course you can meet other learners, share your ideas and join in with active discussions in the comments.

What will you achieve?

By the end of the course, you‘ll be able to...

  • Describe the different types of genomic variants and interpret the impact of different variant types in the context of normal background genomic variation.
  • Apply the tools used in variant classification (including population databases, inheritance data, predictive data, functional data and phenotype) to interpret genomic variation.
  • Apply the American College of Medical Genetics (ACMG) variant interpretation framework (including updates from the Association for Clinical Genomic Science (ACGS) to classify variants in rare disease genes and appraise the outputs.
  • Evaluate the value of the multidisciplinary team (MDT) approach in ensuring high-quality variant interpretation and patient care, and learn how to communicate efficiently in an MDT setting.
  • Evaluate the strengths and weaknesses of each of the tools available for variant interpretation.

Who is the course for?

This course is designed for all health professionals who require knowledge of the basic principles of variant interpretation and applying ACMG guidelines.

This may include: - genomic specialists leading on variant interpretation - clinical scientists - clinical geneticists - genomic counsellors

It will also be useful for genomic champions, eg the clinical specialist who will be attending multi-disciplinary genomic variant interpretation meetings and will need to understand the principles and language of genomic variant interpretation.

Who will you learn with?

I'm a Consultant and Reader in Clinical Genetics. In addition to my clinical role, I am engaged in genomic research and am committed to improving medical education.

I'm a Genetic Counsellor and Honorary Clinical Lecturer in Cancer Genomics.

I am a doctor, based in London and specialising in clinical genetics. I am currently taking time out of clinical practice to focus on supporting and developing resources for genomics education.

Who developed the course?

St George's, University of London

St George’s is the UK’s only university dedicated to medical and health sciences education, training and research.

CanGene CanVar

CanGene CanVar is a five-year Cancer Research UK-funded research program which develops data resources, clinical and educational tools to leverage cancer susceptibility genetic for early detection and prevention of cancer.


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