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:
- Link to the Variant Page in dbVar, in the nstd102 study
- Clinical Significance
- Variant Type
- Variant Length Range
- Mouseover Label
- List of ClinVar Variation Report names
- List of Gene identifiers
- List of Gene symbols
- List of Last evaluated dates
- List of Phenotype identifiers
- List of Phenotypes
- List of Origins
- List of Cytogenetic Band
- List of Review Statuses
- List of Numbers of Submitters
- List of Guidelines
- List of Tested in GTR
- List of Other identifiers
- List of ClinVar RCV accessions
- List of dbVar Variant calls with the same placement, variant type, and clinical significance
- Track Hub date last updated
Variant Colors
The colors indicate variant type, and are based on the dbVar colors described in the dbVar Overview page:
- red:
- blue:
- duplication
- gain
- insertion
- violet:
- light violet:
- light azure:
- brown:
Color Intensity
There are 5 levels of color intensity to indicate levels of clinical significance (showing examples for red/deletions):
- darkest:
- Pathogenic
- Likely pathogenic
- medium-dark:
- medium:
- conflicting data from submitters
- conflicting interpretations of pathogenicity
- medium-light:
- 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:
- acquiring the latest monthly file from: ClinVar XML FTP
- filtering out variants not in scope for dbVar:
- small variants < 50bp
- variants missing genomic placements
- Microsatellite and other types out of scope for dbVar
- generating a unique dbVar variant call for each ClinVar RCV and Allele ID
- generating a unique dbVar variant region for each unique combination of variant call placements
- reformatting and loading ClinVar data to dbVar study nstd102
- assigning dbVar accessions:
- nssv: variant call
- nsv: variant region
- remapping variants to GRCh37 that only had placements in ClinVar on GRCh38 or NCBI36
- remapping variants to GRCh38 that only had placements in ClinVar on GRCh37 or NCBI36
- retrieving latest ClinVar details from: ClinVar Tab-delimited Variant Summary FTP file
- adding length ranges for filtering
- excluding placements not on finished chromosomes
- reducing to non-redundant with respect to placement, variant type, clinical significance
- generating bigBed file
References
- Landrum MJ, et al. ClinVar: public archive of interpretations of clinically relevant variants. Nucleic Acids Research. 2016 Jan 4;44(D1):D862-8. PMID:26582918; PMC:PMC4702865
- Miller DT, et al. Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies. American Journal of Human Genetics. 2010 May 14;86(5):749-64. PMID:20466091; PMC:PMC2869000
- Kaminsky EB, et al. An evidence-based approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabilities. Genetics in Medicine. 2011 Sep;13(9):777-84. PMID:21844811; PMC:PMC3661946
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