Description

This track displays structural variants (SVs) in dbVar that are not classified as common, somatic, or clinical. The track is defined by exclusion: it contains dbVar SVs minus

common variants (covered by the dbVar Common SV track)
variants with somatic origin (covered by the dbVar Somatic SV track)
clinical variants from ClinVar (covered by the ClinVar track)
variants of the types: short tandem repeat, interchromosomal translocation, intrachromosomal translocation
variants from a set of legacy or obsoleted dbVar studies (nstd45, nstd75, nstd90, estd59, estd199, estd214)
variants discovered using low-confidence methods (BAC aCGH, FISH, Karyotyping, MassSpec, Microsatellite genotyping, Multiple complete digestion, Not provided, ROMA, Southern, Western)

NCBI sometimes refers to this category as presumed normal SVs in their hub documentation and source files. We use the term Other here to avoid implying that the variants are clinically normal — the track is purely a residual bucket of dbVar SVs that don't fit the other three composites.

This track is updated with every monthly dbVar release.

Subtracks

The Other SVs are split into two subtracks:

dbVar Healthy SVs: SVs in dbVar with no reported phenotype.
dbVar Phenotype SVs: SVs in dbVar with a reported phenotype, excluding clinical and somatic variants.

The Healthy subtrack is considerably larger than the Phenotype subtrack. Turning on Hide empty subtracks (default) limits the display to subtracks with data in the current viewing window.

Display Conventions and Configuration

Variants are colored by type, using the dbVar color scheme described in the dbVar Overview page:

Color	Variant Type(s)
	deletion, delins, copy number loss
	duplication, copy number gain, insertion
	copy number variation
	inversion
	complex substitution
	tandem duplication
	sequence alteration

Mouseover on items shows gene(s) affected, size, variant type, dbVar study of origin, discovery method, phenotype (in the Phenotype subtrack), and population code (if available).

Subtracks can be filtered by:

Variant Type
Variant Size (Under 10KB, 10KB to 100KB, 100KB to 1MB, Over 1MB)
Discovery Method (Curated, Merging, Multiple, Oligo aCGH, Optical mapping, SNP array, Sequencing, other)
Pathogenic Reciprocal Overlap (none, 10 to 25, 25 to 50, 50 to 75, 75 to 90, 90 to 100) — range of reciprocal overlap with pathogenic variants in nstd102
Population Code (AFR, AMR, EAS, EUR, OTH, SAS, mixed, multiple, none, unknown)

Methods

Per NCBI's dbVar processing pipeline, variant calls are extracted from the variant_calls.gvf files on the dbVar FTP site, reciprocally overlapped with the pathogenic clinical SV file using bedtools, filtered by the exclusion criteria described above, and converted to bigBed format. See the dbVar Overview for full methods.

Data Access

The raw data can be explored interactively with the Table Browser, or the Data Integrator. Due to the size of the Healthy subtrack (over 5 million items), Table Browser queries on large regions may be slow — narrow by chromosome or region where possible.

The data can also be downloaded from 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.

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