VariantValidator is a set of user-friendly software tools designed to validate the syntax and parameters of DNA variant descriptions according to the HGVS Nomenclature
VariantValidator ensures that users are guided through the intricacies of the HGVS Nomenclature, e.g. if the user makes a mistake, VariantValidator automatically corrects the mistake if it can, or provides helpful guidance if it cannot. In addition, VariantValidator accurately inter-converts between transcript variant descriptions and genomic variant descriptions in HGVS and Variant Call Format (VCF).
VariantValidator interfaces with, and substantially builds upon the features of, the hgvs package, used to parse, format, and manipulate biological sequence variants. See https://github.com/biocommons/hgvs/ for details of the hgvs package
VariantValidator can be accessed via our web-hosted User Interface and as a highly functional platform enabling high-throughput and embeddable utilisation of functionality via direct installation or via our REST API which can also be installed locally
The success of the VariantValidator is driven through engagement with you our community of users. We follow an agile development model providing platforms that are used in clinical, education and research practice. Our users test new releases, identify issues and consider improvements which would assist their professional practice. If you spot a bug or have a feature request, contact us via our dedicated support page or via git issues, and we will involve you directly in the planning and acceptance of new resources or bug fixing methodology to ensure your exact needs are met. This helps us to make sure VariuantValidator keeps pace with the fast-moving discipline of genomic medicine.
The basic functionality of https://variantvalidator.org/ and VarinantValidator is documented here
VariantValidator simultaneously and accurately projects genomic sequence variations onto all overlapping transcript reference sequences, and vice versa.
Alternatively, genomic sequence variation can be projected onto a specified single, or specified subset of transcript reference sequences for any given gene.
Projection of sequence variations between reference sequences takes account of discrepancies between genomic and transcript reference sequences, thus ensuring an accurate prediction of the effect on encoded proteins for every gene.
For sequence variations falling within the open reading frames of genes, VariantValidator automatically projects sequence variants via the transcript reference sequence onto genome builds GRCh38, GRCh37, hg38 and hg19 (HGVS format and VCF components), including projection onto relevant Alternative genomic reference sequences, the composition of which varies between patched GRC genome builds and static hg genome builds
Please see LICENSE.txt
Copyright (C) 2016-2024 VariantValidator ContributorsThis program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
You should have received a copy of the GNU Affero General Public License along with this program. If not, see https://www.gnu.org/licenses/.
All contents of VariantValidator are protected by local and international copyright laws. User inputs are submitted for the purpose of interpreting genetic and clinical information (including clinical genomic and genetic data). Outputs returned may or may not have a causal association with disease phenotypes, irrespective of stated classifications or other information presented by VariantValidator. All information returned by VariantValidator, including variant classifications, is subject to change and there is no warranty, express or implied, as to its accuracy, completeness, or fitness for a particular purpose. Use of VariantValidator and information is subject to User responsibility and discretion. Clinical decisions regarding individual patient care should be carried out in conjunction with a healthcare professional with expertise in the relevant genes and diseases. We do not accept any liability for any injury, loss or damage incurred by use of, or reliance on, the information provided by VariantValidator.
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Secure/Remote Access. All access and use of VariantValidator must be made via a secure network.
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Variations in Content. The University of Leicester and the University of Manchester (The Universities) reserve the right, in their reasonable and good faith discretion, to remove or modify materials accessed by VariantValidator or outputs provided by VariantValidator because such materials contain errors or could be subject to an infringement or other adverse claim by a third party.
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Remedial Action. Without limiting the above, The Universities may suspend delivery of the Service if it can be reasonably shown that a User’s failure to comply with this Agreement may cause irreparable harm to them.
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Service Level. The Universities will use reasonable efforts to provide access to the Service on a continuous 24/7 basis (except for regularly scheduled maintenance when Service may be suspended) and free from viruses or other harmful software. The Universities shall not be liable for any failure or delay or interruption in the Service or failure of any equipment or telecommunications resulting from any cause beyond the Universities reasonable control. User is responsible for providing all required information.
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No Warranty. The Universities make no warranty that Service is error free or that the use thereof will be uninterrupted and User acknowledges and agrees that the existence of such errors shall not constitute a breach of this Agreement. The Universities disclaim all other warranties with respect to Service, either express or implied, including but not limited to any implied warranties relating to quality, fitness for any particular purpose or ability to achieve a particular result. Limitation of Liability. Universities total liability for any claims, losses, damages or expenses whatsoever and howsoever caused (even if caused by the Universities negligence and/or breach of contract) shall be limited to the price paid to the Universities for the products or services that are the subject of the User’s claim.
If we find it necessary to change these terms and conditions, including our Privacy Policy and our Terms and Conditions of use, for example to add provisions for a new service, or to curtail problematic use cases, we will provide you with at least either 1 calendar month, or 4 weeks, of notice, before these changes become effective. This notice will be provided via your registered email address. You are responsible for keeping our records of your email address up-to-date, and checking your emails from us, in order to receive such notice in a timely manner. If you continue to use any of the services covered by our terms of service after the notice period, this will be considered to be consent to the new terms of service. This notice period only applies to the terms of service, and does not constrain our right to change the functions of the services we provide, particularly in the case of upgrades, corrections of problematic user behaviour, and other technical issues.
VariantValidator is an Open Source project exclusively funded by grant income and generous contributions from the University of Manchester (UK) and the University of Leicester (UK). In order to apply for external funding and to retain funding from our host institutions we must demonstrate the wider impact of our software throughout the global genomics community. By providing us with some basic information, you are helping us to demonstrate the need for the software and this will help us to build a convincing case which will enable the continued maintenance and future development of this community driven resource.
We will not share any personal data with external organisations. We may use data that you have submitted to build a profile of our users. However, any such profiles will not include any identifiable data e.g. user names or email addresses.
We require an email address for several reasons. The primary reason is to allow us to validate your account, i.e. to ensure that the requested account has originated from a genuine email address. Our batch services require an email address so that results data can be returned to you. Therefore, by creating and verifying your account, we can ensure that your data will only ever be returned to you.
We will only contact you directly for one of five reasons:
- If we receive a direct query from you
- Via automated responses generated by our batch tools
- To inform you about changes to our Terms and Conditions
- To inform you of major changes to our services that may impact your existing workflows
- If our error logs indicate that you might need help in submitting validation requests that will succeed
For any further information, or to ask for help or guidance, please contact us on admin@variantvalidator.org or via our web form.
VariantValidator is a community resource and we represent a diverse range of users. All users and developers must adhere to our Code of Conduct. Violations will be reported and dealt with accordingly.
To accurately cite us, please use both of the follwoing
- Freeman, P.J., Wagstaff, J.F., Fokkema, I.F.A.C. et al. Standardizing variant naming in literature with VariantValidator to increase diagnostic rates. Nat Genet (2024).
https://doi.org/10.1038/s41588-024-01938-w
- Freeman PJ, Hart RK, Gretton LJ, Brookes AJ, Dalgleish R (2018) VariantValidator: Accurate validation, mapping, and formatting of sequence variation descriptions. Hum Mutat. 39(1) 61-68.
VariantValidator Python library VariantValidator will work locally on Mac OS X or Linux-compatible computers. It can also work within a docker container. For installation guidance, see Installation Manuals below.
VariantValidator REST API VariantValidator REST API will work locally on Mac OS X or Linux-compatible computers. It can also work within a docker container For installation guidance, see Installation Manuals below.
Required software:
- MySQL version 5.7 or above
- Python 3.6 or above
- SQLite version 3.8.0 or above
Optional software:
- Postgres version 9.5 or above.
VariantValidator Python library For installation instructions please see INSTALLATION.md.
VariantValidator REST API For installation instructions please see INSTALLATION.md
VariantValidator Python library Please see MANUAL.md. Note that the latest version is not compatible with previous releases.
VariantValidator REST API please see MANUAL.md
Please refer to CONTRIBUTING.md
VariantValidator was developed at the University of Leicester. It is now maintained and developed by the University of Manchester and is hosted (with ongoing development contributions) by the University of Leicester
