ClinVar and our scientific and patient-care community rely on your submissions. With our new Application Programming Interface (API) for submissions, we’ve made it even easier for you to provide us with your most up-to-date classification of variants. The new RESTful API allows you to automate your submission workflow so that you can submit new records and update existing records faster. Setting up your account to use the API requires three one-time activities:
ClinVar Submission API Setup
Click on each of the steps in order to set up your account to use the API!
ClinVar has become a go-to resource for the clinical genetics community. You have come to ClinVar to look for the reported clinical significance of human genetic variants that you’ve identified in clinical testing or through your research. You have researched the supporting evidence and publications to the benefit of the health and genetic science community . You have surveyed all available variants within a gene to understand the spectrum of variation for that gene and to curate gene-disease relationships.
We know how critical this information is to you on a daily basis.
We keep ClinVar free and publicly available and work closely with our submitters to add more variants and supporting information, so that you can continue to benefit from this reliable information at your fingertips.
NCBI and EBI have been hard at work on our joint MANE collaboration, providing a set of representative transcripts for human protein-coding genes that are identically annotated in the NCBI RefSeq and Ensembl/GENCODE annotation sets and exactly match the GRCh38 reference assembly. We’re pleased to announce MANE v0.92, now covering 16,865 genes or ~88% of known human protein-coding genes.
In particular, we’ve focused on clinically relevant genes and MANE Select now includes 99% of genes with high gene-disease validity. This release also includes 43 extra transcripts labeled “MANE Plus Clinical” that we’ve chosen to aid in clinical reporting, for example, when there are additional pathogenic variants not covered in the MANE Select transcript. While it’s critical to consider other alternatively-spliced transcripts for variant interpretation or functional analyses, the MANE Select and MANE Plus Clinical transcripts provide a common foundation for clinical reporting, and other analyses that benefit from using just one well-supported transcript or protein per gene.
You, as a submitter, are the beating heart of ClinVar. Your contributions helps thousands of genetic counselors and clinicians, as well as their patients and patients’ family members. We have added validation to the online file submissions portal, so that you submitters have more control over how to deal with errors in your submitted files.
You now have two options when submitting data. You can submit any data that passes validation and receive a report of the data that failed. The failed data can be reviewed and resubmitted when it’s convenient for you.
In support of data sharing efforts, NCBI’s ClinVar and Genetic Testing Registry (GTR) now accept submissions that use MONDO IDs to identify conditions.
To submit to ClinVar, download our updated spreadsheet templates and enter MONDO as the Condition ID type. Note: The updated template is necessary only if you identify the condition by MONDO ID, not by name.
GTR submitters can use MONDO IDs to identify phenotypes in the clinical tests submitted via spreadsheet, and Mondo phenotype names in both clinical and research test submissions.
“Database resources of the National Center for Biotechnology Information”
by Eric W Sayers, Jeff Beck, J Rodney Brister, Evan E Bolton, Kathi Canese et al. (PMID: 31602479)
The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank® nucleic acid sequence database and the PubMed database of citations and abstracts published in life science journals. The Entrez system provides search and retrieval operations for most of these data from 38 distinct databases. This article provides a brief overview of the NCBI Entrez system of databases, followed by a summary of resources that were either introduced or significantly updated in the past year, including PubMed, PMC, Bookshelf, BLAST databases and more!
We have added a new feature to ClinVar that allows you to follow a particular variant and be notified if the overall clinical interpretation in ClinVar changes, for example from a pathogenic category to a non-pathogenic one. This service will let you know about changes that may require you to update your analysis reports and contact your patients and ordering physicians. The new feature allows you to follow a variant from the variation page (Figure 1). Simply click the “Follow” button to begin receiving notifications.
Figure 1. A ClinVar variant page (VCV000541155.1) showing the ‘Follow’ button. The text on the button changes to ‘Following’ after you add it to your followed variants. Clicking ‘Following’ presents the option to ‘Unfollow’, which removes the variant from the followed list when clicked.
Check out the latest videos on YouTube to learn how to best use NCBI graphical viewers, SRA, PGAP, and other resources.
Genome Data Viewer: Analyzing Remote BAM Alignment Files and Other Tips
This video shows you how to upload remote BAM files, and succinctly demonstrates handy viewer settings, such as Pileup display options, and highlights the very helpful tooltips in the Genome Data Viewer (GDV). There’s also a brief blog post on the same topic.
ClinVar is proud to announce the submission of the one millionth record to its database.
The millionth submission was published on Friday, December 20, 2019, a milestone achievement for providing open access to human variant data with asserted consequence to the clinical genetics and research communities.
ClinVar extends its thanks to the many laboratories, partners, and members of the community whose efforts and adoption of the practice of data-sharing paved the way for this achievement. All organizations that contributed to ClinVar’s genetics resources share in this accomplishment, with special recognition reserved for ClinGen and several of their members, including EGL Genetic Diagnostics/Eurofins Clinical Diagnostics, GeneDx, Invitae, and Laboratory for Molecular Medicine/Partners HealthCare Personalized Medicine, whose early submissions helped jump-start ClinVar’s database.