Tag: ClinVar

ClinVar annotations now available in NCBI Genome Browsers

Do you need to know which of the many NCBI dbSNP variants annotated near your region of interest are likely to be functionally or clinically significant? Figure it out with the track labelled  ‘ClinVar variants with precise endpoints’, available on sequence display viewers at NCBI, including the Genome Data Viewer (GDV) and Variation Viewer!

This track shows variation annotation, including single nucleotide variants and other short variants (e.g. insertions, deletions, etc.) in the NCBI ClinVar database and provides pathogenicity and other metadata. The ClinVar track is displayed next to the default NCBI and Ensembl gene annotation tracks and other NCBI-provided dbSNP and RNA-seq expression tracks.

screenshot of Genome Data Viewer with 'ClinVar variants' track displayed
Figure 1. GDV showing ‘ClinVar variants with precise endpoints’ track next to NCBI human gene annotation. Tracks are color coded for quick and easy interpretation. Legend is also provided.

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NCBI on YouTube: ClinVar API, check data with GaPTools, get genetic context with Sequence Viewer

Every so often, we gather our most recent videos in one post on the blog, for your convenience. Scroll down – and don’t forget to subscribe to our channel!

Introducing GaPTools for dbGaP Submitters

This video introduces new standalone software called GaPTools, which you can use to check your data before submitting to dbGaP. GaPTools uses the same preliminary validation checks as the dbGaP submission portal.

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Automate your workflow with the ClinVar Submission API

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!

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ClinVar Reaches One Million Variants!

A counter ticks up to 1,000,000. Text reads "Celebrating 1,000,000 variants in ClinVar"

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.

Today, we are proud to announce that ClinVar has passed the milestone of one million variants in our database. Continue reading “ClinVar Reaches One Million Variants!”

NCBI RefSeq and Ensembl/GENCODE taking MANE mainstream with v0.92!

NCBI and EBI have been hard at work on our joint MANE collaborationproviding 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.

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New Automated Validation in ClinVar Submission

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.

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Identify conditions in ClinVar and Genetic Testing Registry with MONDO IDs

Identify conditions in ClinVar and Genetic Testing Registry with MONDO IDs

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.

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Canonical SPDI notation now in ClinVar

Did you know that you can see canonical SPDI notation – SPDI notation expressed on the GRCh38 chromosomal sequence – in ClinVar?

Figure 1. The canonical SPDI is provided within the “Variant details” tab. This is just one of many ways to see the notation.

This allows you to easily make connections between output from NCBI’s Variation Services and ClinVar data.

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Read about NCBI resources in 2020 Nucleic Acids Research database issue

The 2020 Nucleic Acids Research database issue features papers from NCBI staff on GenBank, ClinVar and more. These papers are also available on PubMed. To read an article, click on the PMID number listed below.

“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, BookshelfBLAST databases and more!

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New in ClinVar – notifications for changes in the clinical interpretation of variants

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.

FollowFigure 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.

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