Description
Variants from the dbVar study nstd186 (NCBI Curated Common Structural Variants) with reciprocal overlap of Pathogenic variants in nstd102 (Clinical Structural Variants).
NOTE: nstd186 is a curated collection of structural variants from studies with at least 100 samples, include allele frequency data, and have an allele frequency of >=0.01 in at least one population.
nstd102 is derived from structural variants in ClinVar longer than 50bp. For questions about dbVar track data, please contact dbvar.
Data Updates
This track is updated whenever either nstd186
or nstd102 is updated.
nstd186 is updated whenever one of its component studies is updated.
nstd102 is updated monthly following the monthly release of ClinVar.
This track contains data from the following studies:
Subtracks
There is only one subtrack:
Non-Redundant
This track is non-redundant with respect to placement and common variant. The label contains the ClinVar Name of the pathogenic variant with the highest reciprocal overlap range. The detail fields contain the highest reciprocal overlap range and the list of overlapping pathogenic variants.
Display Conventions and Configuration
Labels
The variant label is the dbVar variant call accession (nssv) of the variant in nstd186 (NCBI Curated Common Structural Variants).
Mouseover
The mouseover (displayed when the mouse is hovered over a variant) shows the following:
Detail Page
The detail page contains the following:
- Link to the dbVar Variant Page of the common variant in the dbVar nstd186 study
- Highest Range of Reciprocal Overlap with Pathogenic Variant
- Variant Type
- Variant Length Range
- Mouseover Label
- Global Allele Frequency
- Global Allele Frequency Range
- Link to the dbVar Variant Pages of the overlapping pathogenic variants in the dbVar nstd102 study
- Track Hub date last updated
Variant Colors
The colors indicate variant type of the common variant, and are based on the dbVar colors described in the dbVar Overview page.
- red:
- blue:
- duplication
- gain
- insertion
- violet:
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 track can be filtered by the following:
- Frequency Range
- Variant Length Range
- Range of Reciprocal Overlap with Pathogenic Variant
- Variant Type
Statistics
Counts per subtrack for each filter value:
Frequency Range
| Value |
conflict_pathogenic |
| 0.02 to 0.05 |
295 |
| 0.05 to 0.1 |
159 |
| 0.1 to 0.2 |
111 |
| 0.2 to 0.5 |
140 |
| Over 0.5 |
94 |
| Under 0.02 |
308 |
| Total |
1107 |
Variant Length Range
| Value |
conflict_pathogenic |
| 100KB to 1MB |
485 |
| 10KB to 100KB |
390 |
| Over 1MB |
47 |
| Under 10KB |
185 |
| Total |
1107 |
Range of Reciprocal Overlap with Pathogenic Variant
| Value |
conflict_pathogenic |
| 10 to 25 |
661 |
| 25 to 50 |
234 |
| 50 to 75 |
113 |
| 75 to 90 |
68 |
| 90 to 100 |
31 |
| Total |
1107 |
Variant Type
| Value |
conflict_pathogenic |
| copy number gain |
19 |
| copy number loss |
17 |
| copy number variation |
127 |
| deletion |
557 |
| duplication |
385 |
| insertion |
2 |
| Total |
1107 |
Data Access
Data for this track can be downloaded from the following locations:
- interactively using the UCSC Table Browser
- as BED files from the dbVar Track Hub
Methods
Generating the Conflicts Track consists of the following:
References
See the references for these other tracks in the dbVar Hub:
- Clinical SVs: Clinical Structural Variants in dbVar
- Common SVs: NCBI Curated Common Structural Variants
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