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Paving the Path Towards a Clinical-Grade HGVS Nomenclature Recorded April 29, 2020
Course Information

Paving the Path Towards a Clinical-Grade HGVS Nomenclature -OnDemand

Recorded on Wednesday, April 29, 2020

Date of Release: May 1, 2020

CME, General CEU's, P.A.C.E.® Expiration Date: May 1, 2023

NSGC Credits Expiration Date: May 01, 2022


This session is designed to engage the molecular diagnostic community in a new initiative to improve alignment of the Human Genome Variation Society (HGVS) nomenclature system with laboratory and healthcare provider needs. This effort is driven by CAP’s Genomics Medicine Resource Committee. A brief overview of the history and current operations of HGVS will be provided and speakers will describe variability of the HGVS nomenclature system derived from proficiency testing data sources (Sanger sequencing and NGS challenges). These data clearly demonstrate a need for optimization and a controlled, standardized implementation across clinical laboratories as well as vendors/developers of variant annotation software. The main focus of this session is to collect interactive feedback from the audience on proposed improvements and strategic paths towards widespread global implementation.

Learning Objectives
At the conclusion of this session, participants should be able to:

  1. Review the current variability in the usage of HGVS nomenclature system among clinical laboratories.
  2. Recognize the variability in software tools which generate HGVS nomenclature.
  3. Discuss the need for a version-controlled and optimized HGVS nomenclature for clinical usage.
  4. Outline the CAP proficiency testing challenges (Sanger and NGS) with regard to HGVS nomenclature
  5. Explain potential challenges of health practitioners in understanding HGVS nomenclature



Birgit Funke, PhD, FACMG            Overview

Johan Den Dunnen, PhD               Historic Perspective and Overview of Current HGVS Operations

Ryan J. Schmidt, MD, PhD             Defining the Variability in HGVS Nomenclature Usage in Practice: Results from CAP Proficiency Testing Responses

Somak Roy, MD                            Variant Annotation Software Demonstrate Variability in the HGVS Output

Panelists                                        Walkthrough Improvement Options and Gather Interactive Audience Feedback


Target Audience
Molecular Laboratory Directors, Molecular Pathologists, Trainees, Medical Technologists, Software Developers, Bioinformaticians, Genetic Counselors, Medical Geneticists



Birgit Funke, PhD, FACMG

Associate Professor of Pathology (Part-Time), Harvard Medical School, Massachusetts General Hospital


Johan Den Dunnen, PhD

Leiden University Medical Center


Somak Roy, MD

Assistant Professor of Pathology, and Director of Molecular Informatics and genetics Services at the Division of Molecular and Genomic Pathology, University of Pittsburgh Medical Center (UPMC)


Ryan Schmidt, MD, PhD

Assistant Director of the Clinical Genomics Laboratory in the Center for Personalized Medicine in the Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles

Assistant Professor of Clinical Pathology, Keck School of Medicine of USC


Financial Disclosures

Disclosure Statement

It is the policy of the American College of Medical Genetics and Genomics to plan and implement all of its educational activities in accordance with the ACCME Essentials and Areas and ACCME® Policies to ensure balance, independence, objectivity and scientific rigor. In accordance with the ACCME® Standards for Commercial Support, everyone (speakers, moderators, committee members and staff) who is in a position to control the content of an educational activity certified for AMA PRA Category 1 Credit™ is required to disclose all financial relationships with any commercial interests (see definition below) within the past 12 months that creates a real or apparent conflict of interest. Disclosure must include financial relationships of the individual and those of their spouse/partner. Individuals who do not disclose will be disqualified from participating in a CME activity.

This disclosure pertains to relationships with ACCME-defined commercial interests whose products or services may be related to the subject matter of the presentation topic. Any real or apparent conflicts of interest related to the content of the presentations must be managed prior to the educational activity. ACMG will identify, review and resolve all conflicts of interests prior to an educational activity being delivered to learners.


  • ACMG will follow the ACCME’s expectation that no employees or owners of commercial interests will be involved as planners/faculty/presenters of a CME accredited activity.
  • The ACCME definition of a commercial interest is any entity producing, marketing, re-selling, or distributing health care goods or services consumed by, or used on, patients.
  • The ACCME does not consider providers of clinical service directly to patients to be commercial interests – unless the provider of clinical service is owned, or controlled by, an ACCME-defined commercial interest.
  • Diagnostic laboratories are not considered commercial interests unless they are owned by or have a sister organization which is a commercial interest.


Johan Den Dunnen, PhD
Has no relevant financial relationships to disclose.

Birgit Funke, PhD, FACMG
Has no relevant financial relationships to disclose.

Somak Roy, MD
Dr. Roy has disclosed that he is a consultant for Roche Sequencing Solutions.

Ryan Schmidt, MD, PhD, MS
Has no relevant financial relationships to disclose.

Educational Credit

Claiming your Educational Credits

Complete the activity, score 80% or better on a post test and carefully complete the evaluation form.


Accreditation Statement

The American College of Medical Genetics and Genomics is accredited by the Accreditation Council for Continuing Medical Education (ACCME) to provide continuing medical education for physicians.


Designation Statement

The American College of Medical Genetics and Genomics designates this live activity for a maximum of 1.5 AMA PRA Category 1 Credits™. Physicians should claim only the credit commensurate with the extent of their participation in the activity.


CE (Continuing Education for non-physicians): This activity has been approved for CE credits.
*The certificate is accepted by the ABMGG for certification.


Genetic Counselor Credit

The National Society of Genetic Counselors (NSGC) has authorized American College of Medical Genetics to offer up to 1.5 Category 1 contact hours for the activity ACMG 2020 Digital Edition. The American Board of Genetic Counseling (ABGC) will accept CEUs earned at this program for the purposes of genetic counselor certification and recertification.

ACMG will report completed accredited sessions to NSGC for credit certificates on December 4, 2020, December 3, 2021 and July 8, 2022. Submissions outside of these parameters may incur a processing fee of $35.

P.A.C.E.® CEUs- Laboratory Directors and Laboratory Personnel

ACMG is approved as a provider of continuing education programs in the clinical laboratory sciences by the American Society for Clinical Laboratory Science (ASCLS) Professional Acknowledgment for Continuing Education (P.A.C.E.®) Program. The American College of Medical Genetics and Genomics designates this OnDemand course for a maximum of 1.5 contact hours. ACMG is approved by the Florida Board of Clinical Laboratory Personnel as CE Provider #50-11878. This course is registered # 20-775394 with CEBroker.  ACMG is approved by the California Department of Health Services through the ASCLS P.A.C.E.®


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ACMG follows the ACCME policy on Content Validation for CME activities, which requires:


Content Validation and Fair Balance

  1. ACMG follows the ACCME policy on Content Validation for CME activities, which requires:
  1. All recommendations involving clinical medicine must be based on evidence that is accepted within the profession of medicine as adequate justification for their indications and contraindications in the care of patients.
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  1. Activities that fall outside the definition of CME/CE; “Educational activities that serve to maintain, develop, or increase the knowledge, skills, and professional performance and relationships that a physician uses to provide services for patients, the public, or the profession” (source: ACCME and AMA) will not be certified for credit. CME activities that promote recommendations, treatment, or manners of practicing medicine or pharmacy that are not within the definition of CME/CE or, are known to have risks or dangers that outweigh the benefits or, are known to be ineffective in the treatment of patients.
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When an off-label use of a product, or an investigational use not yet approved for any purpose, is discussed during an educational activity, the accredited sponsor shall require the speaker to disclose that the product is not labeled for the use under discussion, or that the product is still investigational. Discussions of such uses shall focus on those uses that have been subject of objective investigation.



The ACMG does not endorse, or recommend the use of this educational program to make patient diagnoses, particular by individuals not trained in medical genetics. Adherence to the information provided in these programs does not necessarily ensure a successful diagnostic outcome. The program should not be considered inclusive of all proper procedures and tests or exclusive of other procedures and tests that are reasonably directed at obtaining the same results. In determining the propriety of any specific procedure or test, a healthcare provider should apply his or her own professional judgment to the specific clinical circumstances presented by the individual patient or specimen.






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