Description
The track NCBI dbVar Curated Common SVs: Conflicts with Pathogenic highlights loci where
common copy number variants from
nstd186 (NCBI Curated
Common Structural Variants) overlap with structural variants with clinical assertions,
submitted to ClinVar by external labs (Clinical Structural
Variants - nstd102).
Overlap in the track refers to reciprocal overlap between variants in the common
(NCBI Curated Common Structural Variants) versus clinical (ClinVar CNVs)
tracks. Reciprocal overlap values can be anywhere from 10% to 100%.
For more information on the number of variant calls and latest statistics for nstd186 see
Summary of nstd186
(NCBI Curated Common Structural Variants).
Display Conventions and Configuration
Items in this track follow the same conventions as the parent Common SV track: items are colored
by variant type, based on the dbVar colors described in the
dbVar Overview page.
The variant types present in this track are copy number gain, copy number loss, copy number
variation, deletion, and duplication.
| Color |
Variant Type(s) |
| copy number loss, deletion |
|---|
| copy number gain, duplication |
|---|
| copy number variation |
|---|
Mouseover on items indicates genes affected, size, variant type, and allele frequencies (AF).
All tracks can be filtered according to the variant length, variant type and
variant overlap. The overlap filter defines five bins within that range (10-25,
25-50, 50-75, 75-90, 90-100 percent reciprocal overlap; intervals are inclusive of the upper bound).
Data Access
The raw data can be explored interactively with the
Table Browser, or the
Data Integrator. For automated analysis,
the data may be queried from our
REST API.
The data can also be found directly from the dbVar
nstd186 data access, as well as in the
dbVar Track Hub, where additional subtracks are included. For questions about
dbVar track data, please contact
dbvar@ncbi.nlm.nih.gov.
Credits
Thanks to the dbVar team at NCBI, especially John Lopez and Timothy Hefferon for technical
coordination and consultation, and to Christopher Lee, Anna Benet-Pages, and Daniel Schmelter of
the Genome Browser team for engineering the track display.
References
Lappalainen I, Lopez J, Skipper L, Hefferon T, Spalding JD, Garner J, Chen C, Maguire M, Corbett M,
Zhou G et al.
DbVar and DGVa: public archives for genomic structural variation.
Nucleic Acids Res. 2013 Jan;41(Database issue):D936-41.
PMID: 23193291; PMC: PMC3531204