Get “Gene+c.” results in ClinVar


Have you ever searched for a variant in ClinVar with a gene symbol and a c., and wondered why you got no result? Is the variant not in ClinVar, or was something wrong with your search?

Wonder no more – we’ve improved searching in ClinVar so you get results for a gene symbol and c. more often!

While a gene symbol and c. make an ambiguous query and a full HGVS expression is always the best search term, this new service will help you find the variant when gene symbol and c. are all the information that you have.

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ClinVar’s new XML aggregated by Variation ID


Now it’s easier than ever to access all data in ClinVar for a variant or set of variants across all reported diseases.  ClinVar’s new XML is organized by variant only (Variation ID), instead of the variant-disease pair. This reduces redundancy, for example in cases where a variant is related to several disease concepts, and makes the XML consistent with the ClinVar web pages. You can get ClinVarVariationRelease XML from the /xml/clinvar_variation/ directory on the ClinVar FTP site.  New features in ClinVarVariationRelease XML shown in Figure 1 include:

  • Explicit elements to distinguish between variants that were directly interpreted and “included” variants, those that were interpreted only as part of a Haplotype or Genotype. The clinical significance for included variants is indicated as “no interpretation for the single variant”.
  • Explicit elements to distinguish records for simple allele,  haplotypes, and genotypes
  • The Replaces element that provides a history and indicates accessions that were merged into the current accession.
  • A section that  maps the submitted name or identifier for the interpreted condition to the corresponding name used in ClinVar and the MedGen Concept Identifier (CUI)

ClinVarXML_markupFigure 1.  ClinVar variant-centric XML showing a variant record for a haplotype (VCV000236230) that comprises two included variations (SimpleAlleles) that are marked as “no interpretation for the single variant”.  The record includes all the condition records (RCVList) with names and identifiers from MedGen, OMIM and other sources.

To learn more about how to use this data, read our documentation.

Tell us how ClinVar has helped you by writing to us at clinvar@ncbi.nlm.nih.gov.

50,000 new clinically relevant structural variation calls in dbVar


We’ve expanded the catalog of clinically relevant structural variants (SV) in dbVar by adding 57,520 ClinVar records.  You can access the newly added data through study nstd102.

The updated collection includes:

  • 20,000 new SVs, and more than 37,000 copy number variants (CNV) observed in ClinGen laboratories during routine cytogenomic laboratory testing that were previously accessioned separately at dbVar
  • 15,000 SVs asserted as ‘Pathogenic’ or ‘Likely pathogenic’ for thousands of clinical genetic disorders including breast, ovarian, and colon cancers; hypercholesterolemia; schizophrenia; Duchenne Muscular Dystrophy; autism spectrum disorders; and many others
  • links to more than 1,600 related PubMed articles and thousands of related data records in ClinVar, OMIM, GeneReviews, MedGen, MeSH, etc.

You can browse  dbVar studies on the web or download the data.  We provide dbVar data  in a number of standard formats (VCF, GVF, and TSV) mapped to assemblies GRCh38, GRCh37, and NCBI36 allowing you perform analysis using standard tools and integrate the data into your bioinformatic workflows.

Visit our Walkthrough page to learn how to use these new dbVar data to help interpret structural variation in your favorite gene or genomic region.

NCBI at the ACMG meeting in Seattle next week (April 2-6, 2019)


In about a week, NCBI staff will join GeneReviews® on their home turf, Seattle, at the Annual Clinical Genetics Meeting hosted by the American College of Medical Genetics and Genomics (ACMG). While there we will have an exhibit booth (#531) where you can meet our staff, get answers to your questions, and pick-up informative handouts on our various resources for clinical practice.

Also, be sure to visit our two posters on Friday, April 5 from 10:30 AM to 12 PM.

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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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