Clinical SV Track Settings
 
Clinical Structural Variants in dbVar

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 Non-Pathogenic Clinical Structural Variants in dbVar  Clinical Structural Variants in dbVar   Data format 
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 Pathogenic Clinical Structural Variants in dbVar  Clinical Structural Variants in dbVar   Data format 
Assembly: Human Dec. 2013 (GRCh38/hg38)

Description

Variants from the dbVar study nstd102 (Clinical Structural Variants), which is derived from long variants in ClinVar. All variant records were extracted from ClinVar, loaded to dbVar, accessioned, and remapped. This includes only placements on finished chromosomes. Separate subtracks allow distinction between pathogenic and non-pathogenic variants. For questions about dbVar track data, please contact dbvar.

Data Updates

ClinVar releases updated FTP files during the first week of each month. The data is processed in dbVar according to the Methods below, and is released to the public dbVar site, FTP, and public dbVar Track Hub by the end of each month. A detailed summary and history of nstd102 in dbVar can be found in the summary page of ClinVar variants in dbVar.

This track contains the following data:

Subtracks

The long Clinical Structural variants are separated into subtracks according to their pathogenicity:

Non-Redundant

This track is non-redundant with respect to placement, variant type, and clinical significance. The label and detail fields contain the lists of unique values for each field of the redundant variant calls.

Display Conventions and Configuration

Labels

The variant label is the dbVar variant call accession (nssv).

Mouseover

The mouseover (displayed when the mouse is hovered over a variant) shows the following:

  • ClinVar Variant
  • Variant Type
  • Clinical Significance
  • Origin
  • Clinical Phenotypes
  • Total number of redundant calls

Detail Page

The detail page contains the following:

Variant Colors

The colors indicate variant type, and are based on the dbVar colors described in the dbVar Overview page:

Color Intensity

There are 5 levels of color intensity to indicate levels of clinical significance (showing examples for red/deletions):

  1. darkest:
    • Pathogenic
    • Likely pathogenic
  2. medium-dark:
    • Uncertain significance
  3. medium:
    • conflicting data from submitters
    • conflicting interpretations of pathogenicity
  4. medium-light:
    • Benign
    • Likely benign
  5. lightest:
    • not provided
    • association
    • drug response
    • risk factor
    • protective

Placements

For simplicity, the BED files and tracks only contain the variants' outer-most start and stop placements. The actual variant placements may consist of exact start/stop with breakpoint resolution, inner-placements only, outer-placements-only, or some combination. For full details of variant placements, follow the links to the variant pages in dbVar.

Filters

The tracks can be filtered by the following:

  • Clinical Significance
  • Variant Length Range
  • Variant Type

Statistics

Counts per subtrack for each filter value:

Clinical Significance

Value clinvar_non_pathogenic clinvar_pathogenic
Affects 1 0
Benign 21258 0
Benign/Likely benign 186 0
Conflicting interpretations of pathogenicity 45 0
Likely benign 4968 0
Likely pathogenic 0 4401
Likely pathogenic, low penetrance 0 1
Pathogenic 0 21614
Pathogenic, low penetrance 0 5
Pathogenic/Likely pathogenic 0 15
Pathogenic; other 0 1
Uncertain significance 30132 0
Uncertain significance; Pathogenic/Likely pathogenic 0 1
association 20 0
conflicting data from submitters 178 0
drug response 20 0
not provided 773 0
other 2 0
protective 1 0
risk factor 18 0
Total 57602 26038

Variant Length Range

Value clinvar_non_pathogenic clinvar_pathogenic
100KB to 1MB 26439 4296
10KB to 100KB 15967 5035
Over 1MB 4627 8364
Under 10KB 10569 8343
Total 57602 26038

Variant Type

Value clinvar_non_pathogenic clinvar_pathogenic
complex substitution 44 24
copy number gain 25525 3484
copy number loss 22319 7711
deletion 3196 12487
delins 83 287
duplication 6243 1670
insertion 186 351
inversion 5 24
tandem duplication 1 0
Total 57602 26038

Data Access

Data for this track can be downloaded from the following locations:

Methods

Generating the Clinical Structural Variant Tracks consists of the following:

References