Recommendations for clinical interpretation of variants found in non-coding regions of the genome

Abstract

Background: The majority of clinical genetic testing focuses almost exclusively on regions of the genome that directly encode proteins. The important role of variants in non-coding regions in penetrant disease is, however, increasingly being demonstrated, and the use of whole genome sequencing in clinical diagnostic settings is rising across a large range of genetic disorders. Despite this, there is no existing guidance on how current guidelines designed primarily for variants in protein-coding regions should be adapted for variants identified in other genomic contexts.

Methods: We convened a panel of nine clinical and research scientists with wide-ranging expertise in clinical variant interpretation, with specific experience in variants within non-coding regions. This panel discussed and refined an initial draft of the guidelines which were then extensively tested and reviewed by external groups.

Results: We discuss considerations specifically for variants in non-coding regions of the genome. We outline how to define candidate regulatory elements, highlight examples of mechanisms through which non-coding region variants can lead to penetrant monogenic disease, and outline how existing guidelines can be adapted for the interpretation of these variants.

Conclusions: These recommendations aim to increase the number and range of non-coding region variants that can be clinically interpreted, which, together with a compatible phenotype, can lead to new diagnoses and catalyse the discovery of novel disease mechanisms.

Keywords: Gene regulation; Non-coding variation; Variant interpretation.

Fig. 1

Schematic of regulatory elements within and around a gene and examples of disruptions that can lead to disease

Fig. 2

Non-coding region variants are under-ascertained in ClinVar and are more likely to be classified as variants of uncertain significance (VUS) when compared to protein-coding variants. a The proportion of the genomic footprint of MANE transcripts that fall into each of five region categories and the proportion of variants in ClinVar (all, likely pathogenic or pathogenic, likely benign or benign, and VUS) within those regions. b The number of high-confidence pathogenic variants in ClinVar (see ‘2’) that fall into each of the five region categories plotted as bars, with the proportion of variants in each region classified as VUS as blue points

Fig. 3

ACMG evidence framework for non-coding region variants. An adapted version of the figure from Richards et al. [30] (permission granted). Rules that require no extra guidance for non-coding region variants are written in black, with those requiring extra considerations or adaptation in colour. †Should not be applied if the assay only assessed one of multiple possible mechanisms. ^Reduced to supporting following guidance from ClinGen SVI [50]. ^$Variant must have at least as great an impact predicted by in silico tools