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. 2022 Dec;43(12):1808-1815.
doi: 10.1002/humu.24495. Epub 2022 Nov 3.

VariantAlert: A web-based tool to notify updates in genetic variant annotations

Rossano Atzeni  1 , Matteo Massidda  1 , Giorgio Fotia  1 , Paolo Uva  2
Affiliations

VariantAlert: A web-based tool to notify updates in genetic variant annotations

Rossano Atzeni et al. Hum Mutat. 2022 Dec.

Abstract

The reinterpretation of variants based on updated annotations is part of the routine work of research laboratories: the more data is collected about a specific variant, the higher the probability to reinterpret its classification. To support this task, we developed VariantAlert, a web-based tool to help researchers and clinicians to be constantly informed about changes in variant annotations extracted from multiple sources. VariantAlert provides daily re-annotation of variants using external resources accessed through application programming interface, such as MyVariant.info providing in turn links to gnomAD, catalogue of somatic mutations In cancer (COSMIC), ClinVar, CIViC, and many others. Researchers and clinicians can submit one or more lists of variants. If a change is detected for the annotation of a variant due to the upgrade of the underlying resource (e.g., change in gnomAD allele frequency, presence in COSMIC database, change in ClinVar classification) the user is notified by email and updated annotations are stored on the web-site. VariantAlert is freely available at https://github.com/next-crs4/VariantAlert. Installation and deployment are easy thanks to the use of the Docker platform. A Makefile allows you to easily bootstrap VariantAlert. VariantAlert is also available as a web service at https://variant-alert.crs4.it/.

Keywords: clinical genetics; rare diseases; variant annotation; variant reinterpretation; variants of uncertain significance.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
VariantAlert input form. In this page the user can submit a single variant specifying a label for that variant, its genomic coordinates, the genome assembly (hg19, hg38), the reference and alternate alleles, the annotation sources (e.g., CADD, ClinVar). A separate tab is available to submit multiple variants as a batch.
Figure 2
Figure 2
VariantAlert results page containing the list of submitted variants. By clicking the icons in the first column, the user can view, delete or download as an Excel file the complete set of annotations. The submission date and the date a change in annotation has been detected are shown. Unread updates are highlighted with a green mark in the Alerts column.
Figure 3
Figure 3
Example of updated annotations for variant chr1:16254839 C > T. Here the appearance of the variant in ClinVar has been detected (a). The variant is associated with RADIO‐TARTAGLIA syndrome, and it has been reported as pathogenic. (b) Detailed annotations are available by clicking the “Current” section.
See this image and copyright information in PMC

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