Guidelines for copy number variant

So far we presented and discussed single nucleotide changes in the DNA sequence. Here we will focus on the guidelines for investigating copy number variants.

Copy number variant (CNV) classification requires the synthesis and evaluation of evidence from a variety of sources. In order to guide laboratories toward consensus in their classification processes, the American College of Medical Genetics & Genomics (ACMG) and the Clinical Genome Resource (ClinGen) collaborated on a points-based scoring system for the evaluation of constitutional CNVs in 2020. Key evidence types are summarized in Table 1.

Note: *Proband: the first person in a family to be identified as possibly having a genetic disorder and who may receive genetic counselling or testing. The person may have a condition that is thought to be inherited or may be concerned about the risk of developing a genetic condition or passing it to a child.

Table 1. Key evidence types for and against pathogenicity.

A suggested number of points is added or subtracted for each piece of evidence to reflect its relative strength. Ranges are provided to allow for flexibility, as some pieces of evidence are stronger than others, even within the same category. The number of points is totalled and correlated with a classification – pathogenic (e.g., believed to be causative of a Mendelian condition), likely pathogenic, variant of uncertain significance, likely benign, or benign (e.g., not believed to be causative of a Mendelian condition). Full detail, including suggested point values and considerations for upgrading or downgrading points within each category, is available in the publication and its associated supplement.

Briefly, determining the clinical relevance of CNVs depends on whether the gene(s) or specific genomic regions involved are known to be dosage sensitive – whether loss (haploinsufficiency, or HI) or gain (triplosensitivity, or TS) of a given gene or region results in disease. If any gene in the CNV is dosage sensitive, then the entire CNV can be classified as pathogenic (P) (Figure 1).

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Figure 1. Deletions 1-7 (red boxes) overlap genes 1-6 (black boxes) to various degrees. CNVs 1, 2, 3, 4, and 7 can be classified as Pathogenic, as they completely contain Gene 3, which is known to be HI. CNVs 5 and 6, which do not include Gene 3, require further evidence for classification.

Within the ACMG/ClinGen 2020 scoring system, “known” HI or TS genes are defined as those curated as such by the ClinGen evidence-based dosage sensitivity evaluation process, results of which are publicly available. If a CNV completely contains a known HI or TS gene, it receives enough points to be classified as P. If a CNV only partially overlaps a known HI or TS gene, one must assess the possible consequences of the disruption and adjust points accordingly within the suggested scoring ranges. For example, if a deletion overlaps the 3’ end of a known HI gene, it is possible that the resulting protein product would not be expected to undergo nonsense-mediated decay; if this is the case, the CNV may not result in functional loss of the protein, and it may not be appropriate to classify it as P without additional evidence. If no genes or genomic regions within the CNV under evaluation have been evaluated by ClinGen for dosage sensitivity, points for the other pieces of evidence outlined in Table 1 may be used to demonstrate dosage sensitivity for one or more genes/genomic regions therein and guide the final classification.