Description

This track displays common structural variants (SVs) from nstd186 (NCBI Curated Common Structural Variants), divided into subtracks by source study and by population.

nstd186 is a curated collection of structural variants in dbVar from studies with at least 100 samples, that include allele frequency data, and that have an allele frequency of >=0.01 in at least one population. It includes copy number gains and losses, copy number variations, duplications, deletions, insertions, and mobile element variants (ALU, LINE1, SVA, HERV).

The dataset aggregates variants from six source studies:

• gnomAD Structural Variants (nstd166): SVs from the sequencing of 10,847 unrelated individuals in the gnomAD v2.1 release.
• 1000 Genomes Consortium Phase 3 Integrated SV (estd219): SVs from the 1000 Genomes Project Phase 3.
• DECIPHER Consensus CNVs (nstd183): Consensus common population CNVs from high-resolution control sets.
• Lee et al. 2020 (nstd194).
• Abel et al. 2020 (nstd200).
• Byrska-Bishop et al. 2022 (nstd206): High-coverage whole-genome sequencing of the expanded 1000 Genomes sample set.

For the latest nstd186 variant call counts and version history, see the nstd186 summary page at NCBI.

Subtracks

Per-source-study subtracks (variants from nstd186 attributed to one of the six component studies):

• dbVar Curated gnomAD SVs
• dbVar Curated 1000 Genomes SVs
• dbVar Curated DECIPHER SVs
• dbVar Curated Lee SVs
• dbVar Curated Abel SVs
• dbVar Curated Byrska-Bishop SVs

Per-population subtracks (variants with AF >= 0.01 aggregated across nstd186 source studies for each super-population):

• dbVar Curated All Populations (Global)
• dbVar Curated African SVs
• dbVar Curated American SVs
• dbVar Curated East Asian SVs
• dbVar Curated European SVs
• dbVar Curated South Asian SVs
• dbVar Curated Other Pop SVs — samples of mixed, admixed, or uncategorized ancestry that do not map cleanly onto the five super-populations above.

The NCBI dbVar Track Hub additionally provides population-only variants (variants common in one population but not in any other): African only, American only, East Asian only, European only, and South Asian only. These are not loaded as native Genome Browser tracks; connect to the hub to view them.

Display Conventions and Configuration

Items in all subtracks follow the same conventions. Variants are colored by type, using the dbVar color scheme described in the dbVar Overview page:

Color	Variant Type(s)
	copy number loss, deletion (including mobile element deletions)
	copy number gain, duplication, insertion (including mobile element insertions)
	copy number variation

Mouseover on items shows genes affected, size, variant type, allele count (AC), allele number (AN), allele frequency (AF), and population (in per-population subtracks).

Subtracks can be filtered by:

• Variant Type
• Variant Size (Under 10KB, 10KB to 100KB, 100KB to 1MB, Over 1MB)
• Frequency Range (Under 0.02, 0.02 to 0.05, 0.05 to 0.1, 0.1 to 0.2, 0.2 to 0.5, Over 0.5)

The Hide empty subtracks option on the track configuration page hides subtracks that have no data in the current viewing window. This is enabled by default and can be toggled off.

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. 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