Description

This super-track groups structural variant (SV) tracks from dbVar, NCBI's archive of human genomic structural variation. The data are mirrored from the NCBI dbVar track hub.

There are four track collections in this super-track:

• NCBI dbVar Curated Common Structural Variants (dbVar Common SV): Copy-number and other variants from the nstd186 study (NCBI Curated Common Structural Variants), split into subtracks by source study and by population.
• NCBI dbVar Curated Conflict Variants (dbVar Conflict SV): Variants from nstd186 that overlap clinical variants in nstd102 (Clinical Structural Variants).
• NCBI dbVar Somatic Structural Variants (dbVar Somatic SV): SVs with somatic origin, aggregated across six dbVar studies including COSMIC.
• NCBI dbVar Other Structural Variants (dbVar Other SV): SVs in dbVar with no reported phenotype, or with phenotype but not clinical/somatic, excluding variants already present in the Common and Somatic tracks or in ClinVar. NCBI sometimes refers to this category as presumed normal SVs.

Clinical structural variants from dbVar study nstd102 are not duplicated here; they are available in our dedicated ClinVar track (subtrack ClinVar CNVs), which pulls from the same underlying ClinVar XML release.

Source Studies in nstd186 (Common SV)

nstd186 is a curated collection of SVs from studies with at least 100 samples and allele frequency >= 0.01 in at least one population. It aggregates data from six source studies:

• 1000 Genomes Consortium Phase 3 Integrated SV (estd219), added 2016
• gnomAD Structural Variants (nstd166), added 2019 — SVs from the sequencing of 10,847 unrelated individuals (gnomAD v2.1)
• DECIPHER Consensus CNVs (nstd183), added 2020
• Lee et al. 2020 (nstd194), added 2021
• Abel et al. 2020 (nstd200), added 2021
• Byrska-Bishop et al. 2022 (nstd206), added 2022 — high-coverage WGS of the expanded 1000 Genomes sample set

Variants must be of a qualifying structural variant type (deletions, duplications, insertions, copy number variants, and mobile element variants). For the latest statistics and version history, see the nstd186 summary page at NCBI.

Display Conventions

These tracks are composite tracks that contain multiple subtracks. Each subtrack has its own display controls, as described here. Items are colored by variant type using the dbVar color scheme (dbVar Overview):

Color	Variant Type(s)
	deletion, copy number loss
	duplication, copy number gain, insertion
	copy number variation

Some composites display additional colors for less common variant types. Refer to each composite track's description page for the full legend.

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 at the dbVar nstd186 data access page, or in the dbVar Track Hub, where additional subtracks (e.g., population-exclusive variants, ClinVar SVs) are available. 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