Tag: ClinVar

Coming Soon to ClinVar! Somatic Variants & Changes to the XML

Important Note: Support for both the old XML formats has been extended through the end of December 2024. To prepare for these changes, please preview the updated XML schema and supporting documentation on GitHub.

Do you rely on ClinVar XML files for your application or analytical pipeline? We are significantly updating ClinVar’s XML format to support the inclusion of new somatic variation data provided by submitters. In the coming months, you may need to make changes to your tool or pipeline code to continue to use the ClinVar XML.

What will change?

Update to the XML schema
Updates to the VCF and tab-delimited files
Look and feel of the website: new sections to display including somatic classifications
New submission templates for somatic variants, and updates to the submission templates for germline variants

Continue reading “Coming Soon to ClinVar! Somatic Variants & Changes to the XML” →

Celebrating 10 Years of ClinVar: Why it is More Important Than Ever!

Identifying genetic variants and their impact on health is key to tailoring patient care. However, most variants are rare! As such, it is imperative for health care professionals to compare findings from multiple labs, examine evidence, and read related publications to provide accurate interpretations of genetic testing results as well as to develop treatment plans for their patients. ClinVar, a free and publicly available database, was established 10 years ago with this fundamental need in mind.

10 years of ClinVar

The field of variant discovery and classification for diseases has increased rapidly in the last decade! Continue reading “Celebrating 10 Years of ClinVar: Why it is More Important Than Ever!” →

NCBI at ACMG 2023

Join us March 14-18 in Salt Lake City, Utah

We are excited to celebrate ClinVar’s 10th anniversary and look forward to seeing you in-person at the 2023 ACMG Annual Clinical Genetics Meeting, March 14-18, 2023, in Salt Lake City, Utah. We will participate in a variety of events and activities featuring our clinical and human genetic resources.

Check out NCBI’s schedule:

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ClinVar to offer improved support for somatic data

We need your input!

ClinVar is NCBI’s archive of reports of the relationships among human genetic variations and diseases, with supporting evidence. To make ClinVar data more accurate and useful, we are introducing an enhanced data model to better accept and support classifications of somatic variants.

How you can help

Do you have somatic variant classifications to submit to ClinVar? We want to hear from you! We are now testing ClinVar’s enhanced data model and support for classifications of somatic variants. Continue reading “ClinVar to offer improved support for somatic data” →

NEW! Streamlining ClinVar Submission of Assertion Criteria

ClinVar is a freely available submission-driven database for information about genomic variation and its relationship to human health. ClinVar holds more than 1.5 million variants, and is powered by submitters around the world, who provide us with their assessments, the evidence, and the criteria they use to guide their interpretation process and come to their conclusions. To streamline the ClinVar submission process, we are simplifying how submitters provide their assertion criteria. In the past, assertion criteria were provided for each variant. Moving forward, one single set of assertion criteria will be associated with an entire submission regardless of the number of variants. Continue reading “NEW! Streamlining ClinVar Submission of Assertion Criteria” →

New ClinVar graphical display

Maps clinically significant variants by gene and position!

ClinVar is a freely accessible, public archive of reports of the relationships between human variations and phenotypes, with supporting evidence at NLM/NCBI. To help you access your variants of interest quickly, ClinVar is offering an experimental release of an all-new visualization tool in the search results. This graphical display provides an overview of variants when you search by gene or genomic region (Figures 1 and 2).

Currently the graphical display is implemented as an experiment and will appear for only 10 percent of searches by gene or genomic region, but the links in this post will show the display so you can try it out. Alternatively, if you would like to bring up the graphical display for your gene or genomic region search, you can edit the URL in the address bar to change the default gr=0 to gr=1. For example, the following URL with show the graphical display:

https://www.ncbi.nlm.nih.gov/clinvar/?gr=1&term=DSG2[gene]

Note that you can only get the graphical display with gene or genomic region searches. For other types of searches, you will see the table only.

Gene search display

The display for a gene search highlights small variants within the gene. Large structural variants are also marked as a single dot in the middle of the variation. The interactive display shows the placement of variants on the gene and their clinical significance and allows you to zoom in or pan right / left and limit results to variants in a chosen gene. Figure 1 shows the graphical display as it appears at the top of the search results for the desmoglein 2 (DSG2) gene and how to filter and navigate to variants of interest (Search ClinVar: DSG2[gene]).

Figure 1 (A-D). Graphical display views in ClinVar for variants in DSG2, a gene with many known pathogenic variants.

A. Graphical view showing all variants for the DSG2 gene. Results default to the GRCh37 assembly. You can change to the GRCh38 assembly by clicking the arrow at the upper left (circled in red).

B. You can zoom in by mousing over the 8th exon in the gene diagram, which activates a pop-up menu that allows you to re-display only this region by following the link (red box).

C. Refreshed result for the 8th exon of DSG2 showing a number of variants including pathogenic, benign, and ones with conflicting interpretations of pathogenicity. You can select the filters on the left-hand side of the ClinVar result to limit to variants with characteristics of interest, for example Conflicting Interpretations of pathogenicity.

D. Variants in exon 8 of DSG2 filtered for conflicting interpretations of pathogenicity. You can retrieve individual variants by mousing over the graphic to activate the pop-up menu and following the link (red box).

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NCBI ALFA Project at Bio-IT World 2022 Hackathon

Announcing the Allele Frequency Aggregator (ALFA) Project as part of the Bio-IT World 2022 Hackathon: Visualization of NCBI ALFA Variants

Join NCBI at the Bio-IT World 2022 Hackathon on May 4-5, 2022 to learn about and work with data from our ALFA project! The primary goal of this hackathon project is to develop a novel tool, app, or approach to explore and visualize NCBI ALFA variants and allele frequency for 12 different human populations. We aspire to create a new helpful variant interpretation resource for the clinical and research communities.

We hope to see you there! More information and registration here. Continue reading “NCBI ALFA Project at Bio-IT World 2022 Hackathon” →

Using NCBI resources to research, detect, and treat genetic phenotypes

Clinical Genetics Information at Your Fingertips

NCBI offers a portfolio of medical genetics resources to help you research, diagnose, and treat diseases and conditions. You can easily access our data and tools through the Medical Genetics and Human Variation page of the NCBI website. We also encourage you to join our community of thousands of submitters and share your germline and/or somatic data to advance discovery and optimize clinical care.

How and why should you use our resources? Consider the example below.

Your patient is a 40-year-old mother of two presenting with changes in bathroom habits, bleeding, and belly pain. She has a medical history of colonic polyps. Her family history reveals that her maternal grandmother, mother and uncle had several forms of cancers including colon, breast, and endometrium.

Continue reading “Using NCBI resources to research, detect, and treat genetic phenotypes” →

Ten reasons to submit to ClinVar

Wondering why 2,100 submitters from 83 countries have deposited more than 1.9 million records of their latest variation information in ClinVar? Curious about why genetic counselors, physicians, researchers, and so many others enthusiastically use data for nearly 1.2 million unique variants in ClinVar? Thinking about becoming part of this global community and sharing your knowledge to further science and make an impact on patient health? Well, we thought we should help you along by making the case for why everyone should submit to ClinVar.

#1: Every deposit can help a patient

The healthcare community relies on the standardized view offered by ClinVar variant reports, which include interpretations of clinical significance in relation to Mendelian disease, cancer and pharmacogenetics; an aggregated view of interpretations highlighting those in consensus, conflict or reviewed by expert panel; and detailed views of submitter data, including supporting evidence for the interpretation such as phenotype, assertion criteria and references.

Continue reading “Ten reasons to submit to 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.

Continue reading “ClinVar annotations now available in NCBI Genome Browsers” →