DECIPHER SNVs Track Settings
DECIPHER: Chromosomal Imbalance and Phenotype in Humans (SNVs)   (All Phenotype and Literature tracks)

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Data last updated: 2020-10-25


While the DECIPHER database is open to the public, users seeking information about a personal medical or genetic condition are urged to consult with a qualified physician for diagnosis and for answers to personal questions.

Because the UCSC Genes mappings for CNVs are based on associations from RefSeq and UniProt, they are dependent on any interpretations from those sources. Furthermore, because many DECIPHER records refer to multiple gene names, or syndromes not tightly mapped to individual genes, the associations in this track should be treated with skepticism and any conclusions based on them should be carefully scrutinized using independent resources.

Data Display Agreement Notice
These data are only available for display in the Browser, and not for bulk download. Access to bulk data may be obtained directly from DECIPHER ( and is subject to a Data Access Agreement, in which the user certifies that no attempt to identify individual patients will be undertaken. The same restrictions apply to the public data displayed at UCSC in the UCSC Genome Browser; no one is authorized to attempt to identify patients by any means.

These data are made available as soon as possible and may be a pre-publication release. For information on the proper use of DECIPHER data, please see

The DECIPHER consortium provides these data in good faith as a research tool, but without verifying the accuracy, clinical validity, or utility of the data. The DECIPHER consortium makes no warranty, express or implied, nor assumes any legal liability or responsibility for any purpose for which the data are used.

The DECIPHER database of submicroscopic chromosomal imbalance collects clinical information about chromosomal microdeletions/duplications/insertions, translocations and inversions, and displays this information on the human genome map.

This track shows genomic regions of reported cases and their associated phenotype information. All data have passed the strict consent requirements of the DECIPHER project and are approved for unrestricted public release. Clicking the Patient View ID link brings up a more detailed informational page on the patient at the DECIPHER web site.

Display Conventions and Configuration

The genomic locations of DECIPHER variants are labeled with the DECIPHER variant descriptions. Mouseover on items shows variant details, clinical interpretation, and associated conditions. Further information on each variant is displayed on the details page by a click onto any variant.

For the CNVs track, the entries are colored by the type of variant:

  • red for loss
  • blue for gain
  • grey for amplification

A light-to-dark color gradient indicates the clinical significance of each variant, with the lightest shade being benign, to the darkest shade being pathogenic. Detailed information on the CNV color code is described here. Items can be filtered according to the size of the variant, variant type, and clinical significance using the track Configure options.

For the SNVs track, the entries are colored according to the estimated clinical significance of the variant:

  • black for likely or definitely pathogenic
  • dark grey for uncertain or unknown
  • light grey for likely or definitely benign


Data provided by the DECIPHER project group are imported and processed to create a simple BED track to annotate the genomic regions associated with individual patients.


For more information on DECIPHER, please contact


Firth HV, Richards SM, Bevan AP, Clayton S, Corpas M, Rajan D, Van Vooren S, Moreau Y, Pettett RM, Carter NP. DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources. Am J Hum Genet. 2009 Apr;84(4):524-33. PMID: 19344873; PMC: PMC2667985