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Variation Reporter

version 1.4
NCBI Variation Reporter is a tool for accessing the content of human variation resources at NCBI.  You may query our data using your variant calls in a variety of formats.  We will match them to our data to produce a report that draws on dbSNP, dbVar, ClinVar, and NCBI's own human genomic annotation.

Upload your data

The tool accepts input data in the form of variant definitions to query our databases. The data you upload is not a submission, it is not tracked or archived.  You can type/paste your variant calls directly into a text box, or upload them in VCF, HGVS, GVF or BED format files.  To help interpret your data, you must choose an assembly (especially important if you identify chromosome 1 as 'chr1' or just '1'):
  • GRCh37.p13 (hg19)
  • GRCh38 (hg38)

The report will be prepared within the same assembly context as the one you selected.  However, you cannot upload a chromosome position on GRCh38 and select your assembly as GRCh37.p13.

Report Generation

The report we generate includes molecular consequences, 1000Genome minor allele frequencies (MAF), clinical significance and citations.  For novel variants (those not in our archive), we compute molecular consequences based on RefSeq transcripts.  You can browse the first 100 results online, or download a tab delimited file.  Using GRCh37.p13 as your assembly, our report will be on GRCh37.p13, Homo sapiens Annotation release 105.  Using GRCh38 as your assembly, our report will be on GRCh38, Homo sapiens Annotation release 106.

Programatic API

The tool can also be accessed via a programming interface - follow the API instructions.

Get Started

To start, choose an Assembly, and then click on '+' in "Your data" below to upload your variant call files or type the variant call into the text box. Click 'Examples' in the toolbar above, to try out some of our favorites.
Choose your data context
Your data
Available data
No data uploaded yet.
File nameTrack nameAssemblySelectDelete

Define new data for analysis:

Assembly:
Add one HGVS per line here and click upload when you are finished typing.
Or, drag and drop multiple BED, HGVS, GVF or VCF files into the box.
Or, click 'Browse' to find BED, HGVS, GVF, VCF or Wiggle files to add.
Click 'Browse' to find file(s)
Problems
Write to the Help Desk