Clinical SV Track Settings
 
Clinical Structural Variants in dbVar

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Clinical Significance Variant Length Range Variant Type


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 Configure 		 Non-Pathogenic Clinical Structural Variants in dbVar  Non-Pathogenic Clinical Structural Variants in dbVar   Schema 
pack
 Configure 		 Pathogenic Clinical Structural Variants in dbVar  Pathogenic Clinical Structural Variants in dbVar   Schema 

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 4125 0
Benign/Likely benign 186 0
Conflicting interpretations of pathogenicity 48 0
Likely benign 4881 0
Likely pathogenic 0 5561
Likely pathogenic, low penetrance 0 3
Pathogenic 0 26342
Pathogenic, low penetrance 0 7
Pathogenic/Likely pathogenic 0 16
Uncertain risk allele 1 0
Uncertain significance 34957 0
Uncertain significance; Pathogenic/Likely pathogenic 0 1
association 20 0
conflicting data from submitters 178 0
drug response 21 0
not provided 778 0
other 2 0
protective 1 0
risk factor 17 0
Total 45216 31930

Variant Length Range

Value clinvar_non_pathogenic clinvar_pathogenic
100KB to 1MB 24445 5191
10KB to 100KB 9954 6551
Over 1MB 5059 8939
Under 10KB 5758 11249
Total 45216 31930

Variant Type

Value clinvar_non_pathogenic clinvar_pathogenic
complex substitution 44 26
copy number gain 20196 3656
copy number loss 13118 8532
deletion 3810 16774
delins 91 354
duplication 7754 2234
insertion 196 325
inversion 6 29
tandem duplication 1 0
Total 45216 31930

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