Which genetic variants cause disease?

GeneMate

While writing about genetic variants we use the terms benign, pathogenic, and variant of unknown significance (VUS). We’d like to take a moment to describe how genetic variants are classified as such.

The more common genetic sequencing becomes, the more unique genetic variants are discovered. At the time of discovery, these new variants are only known to exist in one or a few individuals in the world. We need a system to help us classify new variants according to their pathogenicity, in other words whether or not they cause disease. In 2015 the American College of Medical Genetics and Genomics (ACMG) published guidelines for variant classification.

Variants are classified on a 5-point scale:

Classification of genetic variants

Definition

1. Benign

Does not cause disease

2. Likely benign

The probability that the variant does not cause disease is greater than 90%

3. Variant of uncertain significance (VUS)

Variants that do not meet the criteria for any other category are classified as VUS

4. Likely pathogenic

The probability that the variant causes disease is greater than 90%

5. Pathogenic

Causes disease

ACMG has developed a set of criteria using typical types of variant evidence to support classification of genetic variants as benign, likely benign, likely pathogenic, or pathogenic.

A variant that occurs in greater than 5 percent of the population is automatically classified as benign. This criterion is strong enough on its own, meaning a variant does not need to meet any additional criteria to earn this classification.

The following are considered strong evidence for benignity:

  • The variant occurs in more individuals than expected in consideration of disease incidence.
  • The variant occurs in healthy individuals, for a disease where all carriers of a disease-causing variant are expected to develop the disease.
  • Studies show that the variant does not impact the protein that the gene codes for.
  • The variant is not correlated with incidence of disease in a family. In other words, both healthy individuals and individuals with disease carry the same variant.

At least two of the above criteria must be met in order to classify a variant as benign.

Lastly, there are seven supporting criteria that together can help classify a variant as likely pathogenic. Variants that meet at least two supporting criteria, alternatively one supporting and one strong, are classified as likely pathogenic.

Different criteria are used to determine pathogenicity. At least two evidence criteria must be met for a variant to be classified as pathogenic. In other words, there is no one criteria strong enough to meet this classification alone. The pathogenicity criteria are categorized as very strong, strong, moderate, or supporting. The following are examples of evidence of pathogenicity:

  • The variant is more common in individuals with disease than in healthy individuals.
  • The variant is not seen in healthy individuals in the general population (or is very rare).
  • Studies show that the variant impacts the protein that the gene codes for.
  • The variant is closely correlated with incidence of disease in a family. In other words, only those who develop disease carry the variant.

Relative to classification of benign variants, there are many more possible criteria combinations that result in a classification of pathogenic or likely pathogenic. Below are some examples:

Pathogenic variant

  • 1 Very Strong + at least 1 Strong
  • 1 Very Strong + at least 2 Moderate
  • 2 Strong
  • 1 Strong + at least 3 Moderate

Likely pathogenic variant

  • 1 Very strong + 1 Moderate
  • 1 Strong + 1–2 Moderate
  • 1 Strong + at least 2 Supporting

Those variants that do not meet the criteria for benign, likely benign, likely pathogenic, or pathogenic are classified as variants of uncertain significance (VUS). This does not mean that a VUS causes disease, or alternatively that it does not, but rather that we lack sufficient evidence to classify it one way or the other. It is important to check for new evidence regularly, as it may allow for reclassification of the VUS as benign or pathogenic. iCellate checks for new evidence every six months.

ACMG recommends that VUS’s not be the basis for clinical care such as admission to screening programs or carrier testing for healthy family members. An individual will therefore not be offered care based on their VUS. Generally, iCellate does not report VUS’s for this reason.

In certain cases, the variant classification sits right on the border between VUS and likely pathogenic. These VUS’s are sometimes given their own subcategory called “VUS+” or “VUS suspicious”. When iCellate identifies a VUS suspicious in someone whose family cancer history suggests the variant could be correlated with disease, we report it. We do this so that the individual may have the opportunity for further investigation in the healthcare system. If the healthcare system determines that the VUS should be further investigated they will initiate a segregation analysis. In such an analysis it is investigated whether the VUS is closely correlated with incidence of disease in the family, which in turn supports pathogenicity.