Tag: ClinVar
ClinVar is pleased to announce that our improved representation of functional data is live on the website, in file submissions, and in downloadable XML files. The following documentation is provided to facilitate future submissions and downloads:
Continue reading “Now Live: Improved Representation of Functional Data in ClinVar!”
As previously announced, NCBI is improving the ClinVar homepage to serve as a better introduction to data and services within the resource. We are also enhancing your search experience in ClinVar!
We are introducing a multiple box search interface where you can enter one or more terms. Each box will be labeled for the type of term that can be entered there. For example, if you search by gene only, you will be able to enter one or more genes in the Gene search box. Each search box will have examples available to demonstrate how to format certain search terms. Continue reading “Coming Soon: ClinVar Search Enhancements”
We are thrilled to announce the NCBI Allele Frequency Aggregator (ALFA) Release 4 (R4), a leap forward in providing comprehensive and robust allele frequency information to the global scientific community. ALFA R4 doubles the cohort size from R3! This expansion offers greater resolution for variant frequencies across diverse populations, improving the utility of ALFA for genetic research and clinical variant interpretation. Continue reading “NCBI ALFA Release 4 Now Available”
Many people visit NCBI’s ClinVar site every day, multiple times a day. As the field of clinical genetics advances, more and more new visitors also come to ClinVar to research the clinical significance of genetic variants. Based on feedback from new and existing customers, we are improving the homepage to serve as a better introduction to data and services within the resource.
Improved ClinVar homepage:
The new ClinVar homepage will allow users to become familiar with the ClinVar data model – how we store and aggregate the data provided by submitters – as well as the organizations that submit data to ClinVar. Visitors can also browse the various methods used to access data in ClinVar. Continue reading “Coming Soon! Enhancements to ClinVar Homepage”
We are pleased to announce the release of the Database of Single Nucleotide Polymorphisms (dbSNP) Build 157, which has approximately 1.2 billion Reference SNP (rs) records across the human genome. This build includes updated datasets from 1000Genomes, TOPMed, gnomAD, NCBI ALFA release 3, and other studies that now incorporate expanded allele frequency data.
Build 157 includes:
All data remain open-access and available for web search, FTP download, and API access. Continue reading “dbSNP Build 157 Release”
The 2025 Nucleic Acids Research Database Issue features papers from NCBI staff on ClinVar, PubChem, GenBank, RefSeq, and more. The citations are available in PubMed with full-text available in PubMed Central (PMC). To read an article, click on the PMCID number listed below.
PMCID: PMC11701734
NCBI provides online information resources for biology, including the GenBank® nucleic acid sequence repository and the PubMed® repository of citations and abstracts published in life science journals. NCBI is currently developing the NIH Comparative Genomics Resource (CGR) to facilitate reliable comparative genomics analyses with an NCBI Toolkit and community collaboration.
Continue reading “NCBI Resources Highlighted in 2025 Nucleic Acids Research Database Issue”
As previously announced, NCBI is improving the way that functional data are submitted to ClinVar and how they are represented in the XML format and on the website. We have started enhancing support for functional data and would like your feedback!
We have updated the GitHub repository with:
Continue reading “Update! Improving the Representation of Functional Data in ClinVar”
NCBI is improving the way that functional data are submitted to ClinVar and how they are represented in the XML format and on the website. Almost half of the variants in ClinVar are variants of uncertain significance (VUS). It’s unclear what clinical action to take for these variants, creating a challenge for clinicians. One potential way to resolve VUS is to develop functional assays to determine the effect the variant has on the gene product, at either the transcript or the protein level. While ClinVar can currently accept functional data, we are striving to make submission easier and more efficient and to make the data easier to find and use. Continue reading “Coming Soon! Improving Representation of Functional Data in ClinVar”
Do you use NCBI’s MedGen? If so, then you probably know it’s NCBI’s one-stop-shop for genetic phenotype information. If you are a healthcare provider, genetic professional, researcher, or anyone who uses MedGen, we want to hear from you to help us make this resource better meet your needs!
We want to know:
NCBI’s ClinVar is now accepting submissions for somatic variants classified for cancer. As recently announced, we updated the ClinVar website as part of our effort to better support the display of submitted somatic variation data.
Access to somatic variation data is essential for understanding tumor biology and will help researchers advance cancer treatment. It also helps clinical cancer testing laboratories provide better patient reports. Make ClinVar as useful for somatic variants as it is for germline by contributing your data! To submit your data, use our new somatic spreadsheet template (SubmissionTemplateSomatic.xlsx) and follow these step-by-step instructions. Once your submission is prepared, you can go to the ClinVar Submission Portal to upload and send your file. See an example below. Continue reading “Submit Your Somatic Variation Data to ClinVar”