The Significance of Unknown Significance: A Teachable Moment

Jeanette J. McCarthy, MPH, PhD; Bryce A. Mendelsohn, MD, PhD


July 05, 2016

The Final Classification

In the case of the SCN1A variant (ie, a single amino acid change, Tyr413Asn, resulting in a change from tyrosine to asparagine at amino acid position 413), the final classification hinges on two key criteria.

Prior Observation of the Variant in Multiple Unrelated Patients With the Same Disease and Absence in Controls (Criterion PS4 in the ACMG Guidelines)

Was this criterion met? The variant was and still is absent from all three major control variant databases used today: 1000 Genomes, Exome Variant Server, and the ExAC Browser. These databases represent the genetic sequences of tens of thousands of ostensibly healthy adults in whom one would not expect to find a dominant, highly penetrant, and pathogenic variant causing an early-onset disease. However, these databases include a thin slice of humanity and are certainly incomplete.

Was the variant observed in multiple other patients with the same phenotype? To answer this question, the laboratory must have access to information about other patients who have undergone genetic testing. Sometimes, these case reports can be found in the published literature. Other times, the cases may be reported in public or private databases. The lack of a centralized, open-access repository of genetic testing results was the driver behind the National Institute of Health's ClinVar database. Unfortunately, not all laboratories contribute their results to ClinVar.

Even if other patients with the same variant are identified, the definitions of "multiple" and "same phenotype" are somewhat subjective. At the time of the Dravet syndrome case, the literature reported two unrelated patients: one with Dravet syndrome[6] and another with alleged vaccine-induced encephalopathy[7] who harbored the very same variant. If these cases were interpreted as "multiple patients with the same phenotype" and then weighed in the context of all the other evidence using the ACMG guidelines, the variant might have been assigned a status of pathogenic.

De Novo Variant With Confirmed Maternity and Paternity (Criterion PS2 in the ACMG Guidelines)

It was well known at the time that variants in SCN1A that cause Dravet syndrome are typically the result of de novo mutations.[8] In other words, the variant that is found in the patient is usually the result of a mutation in the sperm or egg that is not present in either parent. Had the parents undergone genetic testing, this criterion could have been used to sway the interpretation away from being pathogenic (if one parent had the same variant) or toward pathogenic (if the variant was de novo).

The diagnostic laboratory travels only part of the journey that starts with ordering a genetic test and ends with taking clinical action on the basis of the results. The ordering clinician is often left to traverse the remaining distance by understanding the process of variant interpretation, recognizing areas of subjectivity, and actively pursuing means to clarify the results. The point of this exercise is to illustrate the complexities and subjective nature of variant classification even when using a set of professional guidelines on variant interpretation.


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