Variation at NCBI: Resources, Tools and Submissions

We will be summarizing the status of NCBI variation resources and tools.

Variation resources: ClinVar aggregates information about sequence variation and its relationship to human health. dbSNP is a database of common and rare short genetic variations including SNPs and multiple small-scale variations that include insertions/deletions, microsatellites, and non-polymorphic variants. dbVar is a database of genomic structural variation.

Variation Reporter: A tool for accessing the content of NCBI, human variation resources.  You may query our data using your variant calls in a variety of formats.  Reports include molecular consequences, minor allele frequency and clinical attributes.

Variation Viewer: A tool to browse the genome, navigate by gene or exon, filter by variant attributes including allele frequencies from 1000 Genomes or GO-ESP, and integrate with NCBI's molecular databases and medical genetics resources such as ClinVar, MedGen and GTR.  Variant data can be downloaded.  Users can also upload their own variant data to this browser. 

Remap Service: The NCBI Genome Remapping Service is a tool that projects users’ annotation data from one coordinate system to another, including assembly and RefSeqGenes (LRGs) sequences.  The service has both as web and programmatic interface.

Variation Submission: A new online submission system allows users to register their organization and submit files for dbSNP, dbVar or ClinVar. Submissions will be tracked and assigned accessions at NCBI and reports sent back to the user. There is now a single location for all submissions to NCBI variation resources and dbSNP and dbVar accept submission for many animals and plants.