Summary of nstd186 (NCBI Curated Common Structural Variants)

Last updated: Thursday, March 25, 2021.

  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
deletion32,558"nstd186"[study] AND "deletion"[variant_type]
insertion8,725"nstd186"[study] AND "insertion"[variant_type]
alu insertion6,535"nstd186"[study] AND "alu insertion"[variant_type]
copy number variation5,405"nstd186"[study] AND "copy number variation"[variant_type]
duplication4,425"nstd186"[study] AND "duplication"[variant_type]
alu deletion1,094"nstd186"[study] AND "alu deletion"[variant_type]
line1 insertion1,001"nstd186"[study] AND "line1 insertion"[variant_type]
sva insertion478"nstd186"[study] AND "sva insertion"[variant_type]
copy number gain430"nstd186"[study] AND "copy number gain"[variant_type]
copy number loss335"nstd186"[study] AND "copy number loss"[variant_type]
line1 deletion53"nstd186"[study] AND "line1 deletion"[variant_type]
mobile element insertion38"nstd186"[study] AND "mobile element insertion"[variant_type]
sva deletion8"nstd186"[study] AND "sva deletion"[variant_type]
herv deletion1"nstd186"[study] AND "herv deletion"[variant_type]
Total61,086

Variant Calls with Population Frequencies

PopulationTotal Variant CallsQuery
AFR44,088"nstd186"[study] AND "AFR"[population]
ALL61,086"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 %5811,2302,96070.13"nstd186"[study] AND "10 to 25"[pathogenic_overlap_range]
25 to 50 %19455296022.74"nstd186"[study] AND "25 to 50"[pathogenic_overlap_range]
50 to 75 %1031242094.95"nstd186"[study] AND "50 to 75"[pathogenic_overlap_range]
75 to 90 %4527601.42"nstd186"[study] AND "75 to 90"[pathogenic_overlap_range]
90 to 100 %2324320.76"nstd186"[study] AND "90 to 100"[pathogenic_overlap_range]
Total9461,9574,221100

Variant Region Types

Variant Region TypeTotal Variant RegionsQuery
copy number variation38,321"nstd186"[study] AND "copy number variation"[variant_type]
insertion8,570"nstd186"[study] AND "insertion"[variant_type]
mobile element insertion7,934"nstd186"[study] AND "mobile element insertion"[variant_type]
mobile element deletion1,156"nstd186"[study] AND "mobile element deletion"[variant_type]
Total55,981

Variant Region Sources

Variant Region SourceTotal Variant RegionsExample
gnomAD only25,927nsv4634378
DECIPHER only15,211nsv4658010
1000 Genomes only13,468nsv4634381
Lee only961nsv4726775
gnomAD and 1000 Genomes272nsv4634518
gnomAD and Lee141nsv4718556
gnomAD and 1000 Genomes 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
gnomAD_Structural_Variants26,341278,39229,922
DECIPHER Consensus CNVs15,21140,46415,895
1000 Genomes Consortium Phase 3 Integrated SV13,23655,58914,166
Lee et al. 20201,103111,103
Total55,891374,45661,086

nstd186 Load History

Date UpdatedgnomAD version1000 Genomes versionDECIPHER versionLee versionTotal common Variantsnstd186 Variant Callsnstd186 Variant RegionsComment
December, 20202019/10/042016/08/022020/04/172020/08/249,189,32661,08655,981dbVar December 2020 Release
November, 20202019/10/042016-08-022020-04-172020-08-249,188,21261,08656,089dbVar November 2020 Release
October, 20202019/10/042016-08-022020-04-179,188,21259,98355,027October 2020 Release
September, 20202019/10/042016-08-022020-04-179,188,21259,98355,144September 2020 Release
April, 20202019/10/042016/08/02Feb 20209,188,21244,30939,477Loaded gnomAD, 1000Genomes, and DECIPHER
March, 20202019/10/042016/08/029,492,70727,33423,611Loaded gnomAD and 1000Genomes

Data Access

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Last updated: 2021-03-25T16:59:12Z