How to interpret the pathogenicity of a genetic variant

The interpretation of the pathogenicity of genetic variants is a complex process that requires the integration of molecular biology, bioinformatics and clinical knowledge, in order to combine, following a probabilistic approach, basic, epidemiologic and clinical information.

Most laboratories approach the classification following the criteria of the American Board of Medical Genetics (Richards, S et al.  Genet Med 17, 405–423 (2015).  Points are added depending on the evaluation of the following data:

1. Population data: Pathogenic variants should be more frequent in cases than in controls. Pathogenic variants are usually very infrequent in control populations (such as the gnomAD database: https://gnomad.broadinstitute.org/)
2. Computational and predictive data: based in the evaluation of the predicted effects of the variant (coding/non-coding, variants that cause loss of function (truncating, frameshift), conservation and biological relevance of the affected amino acids, and different bioinformatics predictors.
3. Functional data: studies in cells and/or animal models may provide relevant information about the potential pathogenicity of a variant.
4. Segregation data: evaluation of the co-segregation of the variant with disease expression in described families (which should consider different inheritance patterns).
5. De novo genetic variants: variants not present in the parents associated with disease not previously found in the family should receive special consideration.
6. Allelic data: for recessive conditions, the presence in association with other variant affecting other allele, or in homozygosis raises the suspicion
7. Very specific phenotypes: high pre-test probability of an association of a variant in a given gene with the disease, makes the variant more suspicious.

After the evaluation of these data in a “quantitative” way, the variant may be considered definitively pathogenic, likely pathogenic, likely benign or benign, but many variants will be classified as “VUS” or “Variant of Uncertain Significance” that are sometimes defined as those variant with a probability of being pathogenic between 5 and 95%.

Many laboratories consider that those VUS should not be reported, as they do not provide actionable information, and many would not recommend further evaluation in the family. This decision may be controversial and should probably be individualized. If the VUS have a low probability of being pathogenic, and in case of being pathogenic the lack of recognition would not be dangerous for patients and relatives, not reporting (or not making additional studies) is reasonable. But if a VUS has the potential of being dangerous for the patient and/or the relatives, it may be very important to report it and do further studies. An example could be a VUS in the RYR2 gene (associated with catecholaminergic polymorphic ventricular tachycardia) or in the KNCQ1 gene (associated with long QT syndrome) found in an individual with unexplained sudden death.

Clinical and genetic study should likely be considered in first degree relatives, who may be at risk for sudden death in the absence of signs or symptoms of the disease.

The interpretation of the genetic study cannot end with determining the pathogenicity of the identified variants. We need to go a step further to provide information about the clinical consequences of the genetic variant including the age of onset, clinical manifestations and risks associated with its presence. Only with this information we will be able to support correct genetic counselling, risk stratification and clinical management of the disease.