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Summary of nstd186 (NCBI Curated Common Structural Variants)

Last updated: Friday, September 16, 2022.

  1. Methods
  2. Statistics of nstd186 Variants
    1. Variant Call Types
    2. Variant Calls with Population Frequencies
    3. Variant Calls Overlapping Pathogenic Variants
    4. Variant Region Types
    5. Variant Region Sources
  3. Mapping to other dbVar Studies
  4. nstd186 Load History
  5. Data Access

Methods

nstd186 contains Structural Variants (SV) imported from other studies that were originally submitted to dbVar. The criteria for including variants in NCBI Curated Common Structural Variants) are:

Statistics of nstd186 Variants

The following tables reflect current nstd186 status.

Variant Call Types

Variant Call TypeTotal Variant CallsQuery
deletion60,280"nstd186"[study] AND "deletion"[variant_type]
insertion12,806"nstd186"[study] AND "insertion"[variant_type]
duplication12,326"nstd186"[study] AND "duplication"[variant_type]
alu insertion11,380"nstd186"[study] AND "alu insertion"[variant_type]
copy number variation5,730"nstd186"[study] AND "copy number variation"[variant_type]
alu deletion4,874"nstd186"[study] AND "alu deletion"[variant_type]
line1 insertion1,441"nstd186"[study] AND "line1 insertion"[variant_type]
sva insertion758"nstd186"[study] AND "sva insertion"[variant_type]
line1 deletion585"nstd186"[study] AND "line1 deletion"[variant_type]
copy number gain430"nstd186"[study] AND "copy number gain"[variant_type]
copy number loss335"nstd186"[study] AND "copy number loss"[variant_type]
sva deletion173"nstd186"[study] AND "sva deletion"[variant_type]
mobile element insertion57"nstd186"[study] AND "mobile element insertion"[variant_type]
mobile element deletion43"nstd186"[study] AND "mobile element deletion"[variant_type]
herv deletion1"nstd186"[study] AND "herv deletion"[variant_type]
Total111,219

Variant Calls with Population Frequencies

PopulationTotal Variant CallsQuery
AFR44,088"nstd186"[study] AND "AFR"[population]
ALL111,219"nstd186"[study] AND "ALL"[population]
AMR44,088"nstd186"[study] AND "AMR"[population]
EAS44,088"nstd186"[study] AND "EAS"[population]
EUR44,088"nstd186"[study] AND "EUR"[population]
OTH29,922"nstd186"[study] AND "OTH"[population]
SAS14,166"nstd186"[study] AND "SAS"[population]

Variant Calls Overlapping Pathogenic Variants

Counts of variants with at least 10% reciprocal overlap with Pathogenic variants from Clinical Structural Variants (nstd102), based on GRCh38.
Overlap RangeCommon SVsClinical SVsTotal OverlapsPercent of Total OverlapsQuery
10 to 25 %9051,9504,51566.00"nstd186"[study] AND "10 to 25"[pathogenic_overlap_range]
25 to 50 %3359251,57122.96"nstd186"[study] AND "25 to 50"[pathogenic_overlap_range]
50 to 75 %1712824586.69"nstd186"[study] AND "50 to 75"[pathogenic_overlap_range]
75 to 90 %831462073.03"nstd186"[study] AND "75 to 90"[pathogenic_overlap_range]
90 to 100 %4073901.32"nstd186"[study] AND "90 to 100"[pathogenic_overlap_range]
Total1,5343,3766,841100

Variant Region Types

Variant Region TypeTotal Variant RegionsQuery
copy number variation63,566"nstd186"[study] AND "copy number variation"[variant_type]
mobile element insertion13,327"nstd186"[study] AND "mobile element insertion"[variant_type]
insertion12,292"nstd186"[study] AND "insertion"[variant_type]
mobile element deletion3,749"nstd186"[study] AND "mobile element deletion"[variant_type]
Total92,934

Variant Region Sources

Variant Region SourceTotal Variant RegionsExample
Byrska-Bishop only24,860nsv6113156
gnomAD only21,102nsv4634378
DECIPHER only15,211nsv4658065
1000 Genomes only13,360nsv4634386
Abel only11,399nsv5382140
gnomAD and Abel1,983nsv4634764
gnomAD and Byrska-Bishop1,648nsv4635219
gnomAD and Abel and Byrska-Bishop1,194nsv4634380
Lee only892nsv4726801
Abel and Byrska-Bishop694nsv5382619
1000 Genomes and gnomAD166nsv4634575
gnomAD and Lee105nsv4719206
Lee and Byrska-Bishop69nsv4727103
1000 Genomes and gnomAD and Byrska-Bishop43nsv4639265
1000 Genomes and Byrska-Bishop42nsv4642201
1000 Genomes and Abel38nsv4648027
1000 Genomes and gnomAD and Abel38nsv4634518
gnomAD and Lee and Byrska-Bishop36nsv4723515
1000 Genomes and Abel and Byrska-Bishop28nsv4637193
1000 Genomes and gnomAD and Abel and Byrska-Bishop25nsv4640661
1000 Genomes and gnomAD and Lee1nsv4723298

Mapping to other dbVar Studies

All common variants from other studies in have been re-accessioned in NCBI Curated Common Structural Variants (nstd186). A file mapping accessions in other studies to those in nstd186 is available at common_accession_mapping.txt.
StudyVariant Regions matched to nstd186Variant Regions not matched to nstd186Matching nstd186 Variant Calls
Byrska-Bishop et al. 202128,640144,69228,640
gnomAD_Structural_Variants26,341278,39229,922
Abel et al. 202021,493277,59921,493
DECIPHER Consensus CNVs15,21140,46415,895
1000 Genomes Consortium Phase 3 Integrated SV13,23655,58914,166
Lee et al. 20201,103111,103
Total106,024796,747111,219

nstd186 Load History

Date UpdatedTotal common Variantsnstd186 Variant Callsnstd186 Variant RegionsComment
2022-039,661,772111,21992,934replaced old nstd206 with new
2021-089,658,644109,91187,010Loaded Byrska-Bishop version 2021/05/12.
2021-049,488,41882,57968,074Added Abel version 2021/04/08. Added Lee version 2021/01/07.
2020-129,189,32661,08655,981dbVar December 2020 Release.
2020-119,188,21261,08656,089Added Lee version 2020/08/24.
2020-109,188,21259,98355,027October 2020 Release.
2020-099,188,21259,98355,144Added DECIPHER version 2020/04/17.
2020-049,188,21244,30939,477Added DECIPHER version 2020/02.
2020-039,492,70727,33423,611Added gnomAD version 2019/10/04. Added 1000 Genomes version 2016/08/02.

Data Access

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Last updated: 2022-09-16T14:21:14Z