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NCBI Curated Common Structural Variants

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Frequency Range Variant Length Range Variant Type


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 Configure 		 NCBI Curated Common SVs in African Population  NCBI Curated Common SVs in African Population   Schema 
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 Configure 		 NCBI Curated Common SVs in All populations  NCBI Curated Common SVs in All populations   Schema 
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 Configure 		 NCBI Curated Common SVs in All populations from 1000 Genomes  NCBI Curated Common SVs in All populations from 1000 Genomes   Schema 
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 Configure 		 NCBI Curated Common SVs in All populations from Abel  NCBI Curated Common SVs in All populations from Abel   Schema 
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 Configure 		 NCBI Curated Common SVs in All populations from Byrska-Bishop  NCBI Curated Common SVs in All populations from Byrska-Bishop   Schema 
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 Configure 		 NCBI Curated Common SVs in All populations from DECIPHER  NCBI Curated Common SVs in All populations from DECIPHER   Schema 
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 Configure 		 NCBI Curated Common SVs in All populations from gnomAD  NCBI Curated Common SVs in All populations from gnomAD   Schema 
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 Configure 		 NCBI Curated Common SVs in All populations from Lee  NCBI Curated Common SVs in All populations from Lee   Schema 
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 Configure 		 NCBI Curated Common SVs in American Population  NCBI Curated Common SVs in American Population   Schema 
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 Configure 		 NCBI Curated Common SVs in East Asian Population  NCBI Curated Common SVs in East Asian Population   Schema 
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 Configure 		 NCBI Curated Common SVs in European Population  NCBI Curated Common SVs in European Population   Schema 
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 Configure 		 NCBI Curated Common SVs in Other Population  NCBI Curated Common SVs in Other Population   Schema 
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 Configure 		 NCBI Curated Common SVs in South Asian Population  NCBI Curated Common SVs in South Asian Population   Schema 
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 Configure 		 NCBI Curated Common SVs Only in African Population  NCBI Curated Common SVs Only in African Population   Schema 
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 Configure 		 NCBI Curated Common SVs Only in American Population  NCBI Curated Common SVs Only in American Population   Schema 
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 Configure 		 NCBI Curated Common SVs Only in East Asian Population  NCBI Curated Common SVs Only in East Asian Population   Schema 
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 Configure 		 NCBI Curated Common SVs Only in European Population  NCBI Curated Common SVs Only in European Population   Schema 
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 Configure 		 NCBI Curated Common SVs Only in South Asian Population  NCBI Curated Common SVs Only in South Asian Population   Schema 
    

Description

Variants from the dbVar study nstd186 (NCBI Curated Common Structural Variants), which 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. Separate subtracks allow distinction between different populations and original data sources. Allele frequencies are aggregated on these super-populations: global, African, American, East Asian, European, South Asian, other. This track includes copy number variations, gains, duplications, insertions, losses, and deletions. For questions about dbVar track data, please contact dbvar.

Data Updates

nstd186 (NCBI Curated Common Structural Variants) combines data from multiple studies in dbVar. A detailed summary and history of nstd186 can be found in the summary page of Common variants in dbVar.

This track contains data from the following studies:

Subtracks

The NCBI Curated Common Structural variants are separated into subtracks according to population and data source:

Non-Redundant

Except for the _Only_ subtracks, this track is non-redundant with respect to placement and variant type. The label contains the values of the variant with the highest allele frequency at the placement and variant type.

Display Conventions and Configuration

Labels

The variant label is the dbVar variant call accession (nssv).

Mouseover

The mouseover (displayed when the mouse is hovered over a variant) shows the following:

  • List of Affected Genes
  • Position
  • Size
  • Variant Type
  • Allele Count
  • Allele Number
  • Allele Frequency
  • Population (if population-specific track)
  • Total number of redundant calls

Detail Page

The detail page contains the following:

Variant Colors

The colors indicate variant type, and are based on the dbVar colors described in the dbVar Overview page.

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 tracks can be filtered by the following:

  • Frequency Range
  • Variant Length Range
  • Variant Type

Statistics

Counts per subtrack for each filter value:

Frequency Range

Value common_1000g common_abel common_african common_american common_byrska_bishop common_decipher common_east_asian common_european common_global common_gnomad common_lee common_other common_south_asian
0.02 to 0.05 3060 2738 7955 4459 5477 5051 2591 4230 19612 5208 53 4582 1636
0.05 to 0.1 1952 2106 7257 3857 3611 3382 3136 3995 12870 2909 56 2549 1565
0.1 to 0.2 1919 2569 7165 5431 3969 1546 4481 5370 13791 4830 80 4315 1728
0.2 to 0.5 2651 3783 8523 7691 6079 1315 7681 7615 18002 5466 237 5422 2703
Over 0.5 1098 2144 3664 3789 4193 849 4235 3825 10742 2431 654 2518 1200
Under 0.02 3096 2005 1703 3756 5284 3631 1394 1613 17446 5364 22 3522 840
Total 13776 15345 36267 28983 28613 15774 23518 26648 92463 26208 1102 22908 9672

Variant Length Range

Value common_1000g common_abel common_african common_american common_byrska_bishop common_decipher common_east_asian common_european common_global common_gnomad common_lee common_other common_south_asian
100KB to 1MB 86 78 184 185 288 445 173 156 1019 128 0 106 69
10KB to 100KB 1059 481 2455 2281 1744 1872 2035 2172 6652 1706 0 1527 752
Over 1MB 0 1 1 0 11 42 1 0 55 1 0 1 0
Under 10KB 12631 14785 33627 26517 26570 13415 21309 24320 84737 24373 1102 21274 8851
Total 13776 15345 36267 28983 28613 15774 23518 26648 92463 26208 1102 22908 9672

Variant Type

Value common_1000g common_abel common_african common_american common_byrska_bishop common_decipher common_east_asian common_european common_global common_gnomad common_lee common_other common_south_asian
alu deletion 1089 2107 1073 1032 0 0 952 985 3195 0 0 0 1002
alu insertion 4485 0 5645 4298 4844 0 3452 3910 11099 2043 0 1580 3047
copy number gain 303 0 260 253 0 0 219 216 303 0 0 0 239
copy number loss 327 0 278 261 0 0 189 215 327 0 0 0 227
copy number variation 501 0 1513 1497 322 0 1357 1443 1900 1077 0 1025 384
deletion 6040 10041 16682 13420 14003 13897 10732 12320 49672 12435 0 10937 4069
duplication 84 2759 2211 1641 4583 1877 1344 1552 10919 2409 0 1998 41
herv deletion 1 0 1 1 0 0 0 1 1 0 0 0 0
insertion 27 0 7279 5520 4079 0 4421 5071 12287 7587 1102 6835 14
line1 deletion 53 331 53 51 0 0 48 49 383 0 0 0 48
line1 insertion 590 0 830 657 440 0 527 566 1415 410 0 329 398
mobile element deletion 0 0 0 0 43 0 0 0 43 0 0 0 0
mobile element insertion 0 0 34 21 19 0 18 21 56 38 0 33 0
sva deletion 8 107 8 7 0 0 7 7 115 0 0 0 7
sva insertion 268 0 400 324 280 0 252 292 748 209 0 171 196
Total 13776 15345 36267 28983 28613 15774 23518 26648 92463 26208 1102 22908 9672

Data Access

Data for this track can be downloaded from the following locations:

Methods

Generating the NCBI Curated Common Structural Variant Tracks consists of the following:

References