Resource Summary
| Name | Description |
|---|---|
| ClinVar | Reported relationships between human variation and observed health status with supporting evidence |
| dbSNP | Single nucleotide variations, microsatellites, small-scale insertions and deletions, and population-specific frequencies |
| dbVar | Large scale genomic variation, including large insertions, deletions, translocations, and inversions |
| GTR® | Genetic tests and laboratories,with detailed information about the tests such as what is measured and analytic and clinical validity |
| dbGaP | Genome-wide association (GWAS) and other studies which investigate the interaction of genotype and phenotype |
| PheGenI | Search for human phenotype genotype relationships |
| MedGen | An aggregator of terms from multiple, authoritative sources on genetic diseases and conditions, organized into concept groupings and hierarchies |
| GeneReviews® | Expert-authored, peer-reviewed disease descriptions that apply genetic testing to the diagnosis and management of inherited conditions |
| Medical Genetics Summaries (MGS) | Summaries reviewing genetic variants that underlie inherited conditions, disesase risk, and specific drug responses |
| Variation Viewer | A genomic browser for variations by chromosomal location, gene symbol, phenotype, or variant IDs from dbSNP, dbVar, and ClinVar |
| OSIRIS | Quality assurance software package to analyze multiplex short tandem repeat (STR) DNA profiles based on laboratory-specific protocols |
Which tool do I use for .... ?
- I have 3000 variant calls. How do I find out which is possibly significant? - Use Variation Services.
- I am studying my favorite gene. How do I find all variants on that gene? - Use Variation Viewer.
- I have a VCF file in GRCh37 coordinates. How do I move those to GRCh38 coordinates? - Use the NCBI Genome Remapping Service.
- I want to search the NHGRI GWAS Catalog for studies related to Basal Cell Carcinoma. - Use PheGenI.
- I want to access the database for small or large structural variations. - Refer to dbSNP and dbVar FAQs.
NCBI Variation Tools
This is a list of available NCBI Variation Tools for investigating and understanding human variation.
Variation Services
Variation Services is an API for processing medium volume of data (<100K variants). It has functions for searching, normalizing, remapping, and annotating user's variants with dbSNP data. Users that need a high volume of data (>100K variants) can access the dbSNP by FTP.
Variation Viewer
Variation Viewer is a tool for interactive examination and download of nucleotide variants for a specific locus. It supports both the GRCh38 and GRCh37.p13 assemblies. Variation Viewer integrates data from all of the NCBI Variation databases and presents them in a coupled graphical and tabular report. The resulting list of variants can be saved locally using the download function. You can also upload their own variant data to this browser. More information can be found on the NCBI Variation Viewer Fact sheet and in an introductory video tutorial.
NCBI Genome Remapping Service
The NCBI Genome Remapping Service is a tool that projects users' annotation data from one coordinate system to another. With the Assembly-Assembly remap, you can remap your variant calls between different assembly versions, while the Clinical Remap permits you to remap data between RefSeqGenes or LRGs and an assembly, using NCBI calculated alignments. More information can be found on the NCBI Remap Service fact sheet. The remapping service has a web interface as well as an API for bulk processing.
PheGenI
The Phenotype-Genotype Integrator (PheGenI) is a tool that integrates the search and retrieval of associated genotype-phenotype data from National Human Genome Research Institute (NHGRI) Genome-wide Association Study (GWAS) Catalog integrated with data housed in Gene, dbGaP, OMIM, GTEx and dbSNP. It provides search by genotype and phenotype. The dbSNP Data in NCBI PheGenI is only mapped GRCh38 at this time. More information can be found on the NCBI Phenotype-Genotype Integrator fact sheet.