Improved ClinVar search quickly connects you to information about variants


If you’ve been searching in ClinVar, you might have noticed search improvements introduced in December that reliably connect you with information on your variant of interest. ClinVar has broadened its search capability to accept many different ways of expressing the same variation, including variation described on RefSeq transcripts and proteins. If your variant expression  is not reported in ClinVar, we alert you to other variants at the same genomic location or link you to related information in other NCBI resources such as dbSNP, LitVar, and PubMed. ClinVar will also now interpret expressions that contain minor errors or warn you about improper syntax that it cannot interpret.

sensor2Figure 1.  Improved search results in Clinvar showing mapping of an HGVS expression to the equivalent variant in ClinVar.

Here are some example queries that show the improved search results.

NM_001318787.1:c.2258G>A – an HGVS expression that is not in ClinVar, but ClinVar has an alternate expression for a variant (Figure 1).

NM_004958.3:c.7365C>A – a variant not in ClinVar, but another variant is at the same genomic location is in ClinVar.

NM_002113.2:c.19delG – a variant is not in ClinVar, but there is additional information for the variant in other databases.

We welcome your feedback on your search experience and any additional ideas on how to improve searching in ClinVar.

February 6 Webinar: New Variation Services for Normalizing, Remapping, and Annotating Variants


Join us on Wednesday, February, 2019, when NCBI staff will show you how to use a new set of NCBI variation services that rely on a variant data model called SPDI (Sequence Position Deletion Insertion). These services and data model allow you to inter-convert, map and disambiguate variants in standard formats (RefSNP accessions, HGVS and VCF). Unlike many current variant notation systems, SPDI provides unambiguous, machine-readable definitions of variants. SPDI not only powers SNP build and mapping procedures at NCBI but also our variant sensors that are active in the global search and ClinVar. These services and notation system provide valuable new tools for people who work with sequence variants.additional variant information.

Date and time: Wed, Feb 6, 2019 12:00 PM – 12:30 PM EDT

Register

After registering, you will receive a confirmation email with information about attending the webinar. A few days after the live presentation, you can view the recording on the NCBI YouTube channel. You can learn about future webinars on the Webinars and Courses page.

Update single records easily with ClinVar’s Single SCV Update


The ClinVar Team is happy to announce a new online form in the ClinVar Submission Portal, the Single SCV Update, which makes it easier for you to update a single record.

ClinVar_SIngle_SCV_2The new ClinVar Single SCV Update form showing the sections for editing the evaluation date, clinical significance, condition, and citations.

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MedGen: Your search engine for human medical genetics


MedGen is a free, comprehensive resource for one-stop access to essential information on phenotypic health topics related to medical genetics as collected from established high-quality sources. It integrates terminology from multiple primary ontologies (or nomenclatures) to facilitate standardization and more accurate results from search queries.

Some things you can do in MedGen:

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NCBI presents resources for genetic counselors at NSGC 2018


Today, November 8, National Society of Genetic Counselors (NSGC) celebrates the second annual Genetic Counselor Awareness Day. At NCBI, we’ve been working hard to provide and improve resources, such as MedGen, Genetic Testing Registry (GTR), ClinVar, and Medical Genetics Summaries (MGS), to help genetic counselors.

Next week, NCBI staff will be at the NSGC 2018 conference in Atlanta, GA. While there, you can chat in person with us at booth #700 to learn about our medical genetics resources and pick up helpful material. We’d also love to hear any other questions or feedback to help support you.

To stay up-to-date about NCBI staff at NSGC 2018 follow us on Twitter at @NCBI_Clinical ‏and @NCBI. For more information about other NCBI presentations at NSGC, check the Conferences and Presentations page.

Discover GTR at AMP 2018 (Nov 1-3)


Starting this Thursday, November 1st, NCBI staff from projects like ClinVar, GTR, MedGen, Medical Genetics Summaries and OSIRIS will be ready to hear your feedback at the Association for Molecular Pathology (AMP) 2018 Annual Meeting & Expo in San Antonio, Texas. Come to booth #1810 and tell us how to make our resources better for you or ask questions about how to participate and use these resources!

Staff will also present on their current work at AMP 2018. We will present our analyses of current GTR tests and discuss how GTR data aims to reflect the current genetic testing landscape.

Below is a sneak peek on two different presentations to learn about “The NIH Genetic Testing Registry (GTR): Test Methodologies as a Sensor of the Precision Medicine Environment”:

  • Poster TT046 – Friday, November 2 from 2:30 – 3:30 PM
  • Technical Topics Platform Presentation – Saturday, November 3 from 7:45 – 8:00 AM

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NCBI at ASHG 2018: Data and Clinical CoLabs introduce interactive graphical displays and medical genetics resources


As you know, NCBI will be attending American Society of Human Genetics (ASHG) 2018 in San Diego.

This year, we have two CoLabs – interactive sessions where you can learn about freely available NCBI tools and resources. Read on below for a description of each CoLab and join us at ASHG in two weeks!

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October 10 Webinar: Using NCBI Medical Genetics Resources: MedGen, ClinVar, GTR


Next Wednesday, October 10, 2018,  NCBI staff will show you how to use the NCBI resources MedGen, ClinVar, and GTR to locate records for a specified list of symptoms or clinical features, explore specific disease-causing variants, see the review status of the clinical significance for a genetic variant, and find tests relevant to a clinical feature, gene or disease. You will also learn which resource works best for different types of searches.

Date and time: Wed, Oct 10, 2018 12:00 PM – 12:45 PM EDT

Register

After registering, you will receive a confirmation email with information about attending the webinar. A few days after the live presentation, you can view the recording on the NCBI YouTube channel. You can learn about future webinars on the Webinars and Courses page.

Going to ASHG? Here’s a sneak peek at our ClinVar poster


This October, some NCBI staff will head out to present at the American Society of Human Genetics (ASHG) conference in sunny San Diego. Below, we give you an inside scoop on the ClinVar poster that we’ll present at ASHG.

Want to learn more about how you can submit phenotype and functional data? Or access the data?

Have we hooked you yet?

Head to Poster 1492T “Increasing phenotypic and functional evidence in ClinVar” on Thursday, Oct. 18 from 3 PM to 4 PM. (Exhibit Hall, Ground Floor)

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Standalone variation services replace Variation Reporter


As of July 2018, a new set of standalone variation services replaces the variant matching functions of Variation Reporter. Variation Reporter was a tool designed to search human sequence variation data by location and to report matching variants found in dbSNP, dbVar, and ClinVar.

The new services are faster, better at handling variants in repeat regions, and scalable to accommodate the continued explosive growth of variation volume. You can find more information about the services in the initial blog post and online SPDI document.

If you would like to report any issues related to these new services and/or would like to provide comments, please write to snp-admin@ncbi.nlm.nih.gov.

If you have any specific questions about the NCBI site in general, contact us at info@ncbi.nlm.nih.gov.

We appreciate your continued support and interaction with the NCBI tools.