Tag: ClinVar

Coming Soon! Updates to the ClinVar Website

In order to support the inclusion of submitted somatic variation data, we are updating the ClinVar website. In early 2024, you will begin to see some changes.

What will change?

Variant (VCV) record pages will have an updated look and feel:

Simpler layout with no tabs
New sections will display somatic classifications
- Summary section will be divided into germline classification and display the two types of classifications for somatic variants – somatic clinical impact and oncogenicity
- Sections for conditions, submitted records, functional evidence, and citations will be provided for both germline and somatic classifications
- A toggle will allow you to select and show just information pertaining to germline or somatic data

Continue reading “Coming Soon! Updates to the ClinVar Website” →

Using NCBI Resources for Genotype-Based Medication Optimization

NCBI offers a variety of clinical genetic resources to help you research, diagnose, and treat diseases and conditions. You can quickly and easily access our data and tools through the Medical Genetics and Human Variation page of the NCBI website.

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

Your patient is a 58-year-old woman who has been diagnosed with Acute Coronary Syndrome, scheduled for an angioplasty, and she will need to take clopidogrel for at least three months. She mentions that her father died of a stroke while taking the drug and is concerned. You look into pharmacogenetic influences on clopidogrel response and use the results of your patient’s genetic test to determine if a change in the prescription is needed. Continue reading “Using NCBI Resources for Genotype-Based Medication Optimization” →

Join NCBI at ASHG 2023

November 1-5 in Washington, D.C.

We look forward to seeing you in person at the American Society for Human Genetics Annual Meeting (ASHG 2023), November 1-5, 2023, in Washington, D.C. We will participate in a variety of activities and events including hosting an exhibit booth where you can stop by to meet NCBI experts, ask questions, provide feedback, or just chat! We’re especially excited to share our recent efforts on our clinical and human genetic resources and provide an update on the NIH Comparative Genomics Resource (CGR).

Check out NCBI’s schedule of activities and events:

Continue reading “Join NCBI at ASHG 2023” →

ClinVar Partners with ClinGen to Review & Curate Submitted Records

Do you currently use or submit clinical variation data? NCBI now has a new mechanism to improve ClinVar data quality. Since ClinVar’s founding over 10 years ago, the amount of information in this free resource has expanded dramatically with submissions from research and clinical laboratories all over the world. Because of the large volume of data and the importance of data quality, we are working with ClinGen biocurators to address problematic records for variants that do not require the efforts of an expert panel.

What’s new?

ClinVar and ClinGen have established a new process for ClinGen biocurators to review submitted records in ClinVar. A problematic record will be curated by ClinGen as a candidate to be flagged in ClinVar. We will notify relevant submitters giving them an opportunity to review and update their data. If the submitter does not provide an update, the problematic record will be flagged in ClinVar, so that it does not contribute to the overall classification. The record, however, will remain accessible in the database (Figure 1). This will reduce the number of variants with a conflict in the classification and improve the accuracy of the ClinVar dataset. Continue reading “ClinVar Partners with ClinGen to Review & Curate Submitted Records” →

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

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:

Continue reading “NCBI at ACMG 2023” →

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).

Continue reading “New ClinVar graphical display” →