Summary of nstd186 (NCBI Curated Common Structural Variants)

Last updated: Monday, September 18, 2023.

Methods
Statistics of nstd186 Variants
Mapping to other dbVar Studies
nstd186 Load History
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:

studies: only include variants from the following dbVar studies:

variant types: include variants with these variant call types:

alu deletion
alu insertion
copy number gain
copy number loss
copy number variation
deletion
duplication
herv deletion
insertion
line1 deletion
line1 insertion
mobile element insertion
sva deletion
sva insertion

frequency: only include variant calls with:

Allele Frequency >= 0.01
at least 100 samples.

Statistics of nstd186 Variants

The following tables reflect current nstd186 status.

Variant Call Types

Variant Call Type	Total Variant Calls	Query
deletion	60,280	"nstd186"[study] AND "deletion"[variant_type]
insertion	12,806	"nstd186"[study] AND "insertion"[variant_type]
duplication	12,326	"nstd186"[study] AND "duplication"[variant_type]
alu insertion	11,380	"nstd186"[study] AND "alu insertion"[variant_type]
copy number variation	5,730	"nstd186"[study] AND "copy number variation"[variant_type]
alu deletion	4,874	"nstd186"[study] AND "alu deletion"[variant_type]
line1 insertion	1,441	"nstd186"[study] AND "line1 insertion"[variant_type]
sva insertion	758	"nstd186"[study] AND "sva insertion"[variant_type]
line1 deletion	585	"nstd186"[study] AND "line1 deletion"[variant_type]
copy number gain	430	"nstd186"[study] AND "copy number gain"[variant_type]
copy number loss	335	"nstd186"[study] AND "copy number loss"[variant_type]
sva deletion	173	"nstd186"[study] AND "sva deletion"[variant_type]
mobile element insertion	57	"nstd186"[study] AND "mobile element insertion"[variant_type]
mobile element deletion	43	"nstd186"[study] AND "mobile element deletion"[variant_type]
herv deletion	1	"nstd186"[study] AND "herv deletion"[variant_type]
Total	111,219

Variant Calls with Population Frequencies

Population	Total Variant Calls	Query
AFR	44,088	"nstd186"[study] AND "AFR"[population]
ALL	111,219	"nstd186"[study] AND "ALL"[population]
AMR	44,088	"nstd186"[study] AND "AMR"[population]
EAS	44,088	"nstd186"[study] AND "EAS"[population]
EUR	44,088	"nstd186"[study] AND "EUR"[population]
OTH	29,922	"nstd186"[study] AND "OTH"[population]
SAS	14,166	"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 Range	Common SVs	Clinical SVs	Total Overlaps	Percent of Total Overlaps	Query
10 to 25 %	905	1,950	4,515	66.00	"nstd186"[study] AND "10 to 25"[pathogenic_overlap_range]
25 to 50 %	335	925	1,571	22.96	"nstd186"[study] AND "25 to 50"[pathogenic_overlap_range]
50 to 75 %	171	282	458	6.69	"nstd186"[study] AND "50 to 75"[pathogenic_overlap_range]
75 to 90 %	83	146	207	3.03	"nstd186"[study] AND "75 to 90"[pathogenic_overlap_range]
90 to 100 %	40	73	90	1.32	"nstd186"[study] AND "90 to 100"[pathogenic_overlap_range]
Total	1,534	3,376	6,841	100

Variant Region Types

Variant Region Type	Total Variant Regions	Query
copy number variation	63,566	"nstd186"[study] AND "copy number variation"[variant_type]
mobile element insertion	13,327	"nstd186"[study] AND "mobile element insertion"[variant_type]
insertion	12,292	"nstd186"[study] AND "insertion"[variant_type]
mobile element deletion	3,749	"nstd186"[study] AND "mobile element deletion"[variant_type]
Total	92,934

Variant Region Sources

Variant Region Source	Total Variant Regions	Example
Byrska-Bishop only	24,860	nsv6112823
gnomAD only	21,102	nsv4634378
DECIPHER only	15,211	nsv4658010
1000 Genomes only	13,360	nsv4634381
Abel only	11,399	nsv5381825
gnomAD and Abel	1,983	nsv4634383
gnomAD and Byrska-Bishop	1,648	nsv4634398
gnomAD and Abel and Byrska-Bishop	1,194	nsv4634380
Lee only	892	nsv4726775
Abel and Byrska-Bishop	694	nsv5381863
1000 Genomes and gnomAD	166	nsv4634575
gnomAD and Lee	105	nsv4718556
Lee and Byrska-Bishop	69	nsv4726811
1000 Genomes and gnomAD and Byrska-Bishop	43	nsv4636539
1000 Genomes and Byrska-Bishop	42	nsv4635069
1000 Genomes and Abel	38	nsv4634874
1000 Genomes and gnomAD and Abel	38	nsv4634518
gnomAD and Lee and Byrska-Bishop	36	nsv4718801
1000 Genomes and Abel and Byrska-Bishop	28	nsv4635009
1000 Genomes and gnomAD and Abel and Byrska-Bishop	25	nsv4635514
1000 Genomes and gnomAD and Lee	1	nsv4723298

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.

Study	Variant Regions matched to nstd186	Variant Regions not matched to nstd186	Matching nstd186 Variant Calls
Byrska-Bishop et al. 2022	28,640	144,692	28,640
gnomAD_Structural_Variants	26,341	278,392	29,922
Abel et al. 2020	21,493	277,599	21,493
DECIPHER Consensus CNVs	15,211	40,464	15,895
1000 Genomes Consortium Phase 3 Integrated SV	13,236	55,589	14,166
Lee et al. 2020	1,103	11	1,103
Total	106,024	796,747	111,219

nstd186 Load History

Date Updated	Total common Variants	nstd186 Variant Calls	nstd186 Variant Regions	Comment
2022-03	9,661,772	111,219	92,934	replaced old nstd206 with new
2021-08	9,658,644	109,911	87,010	Loaded Byrska-Bishop version 2021/05/12.
2021-04	9,488,418	82,579	68,074	Added Abel version 2021/04/08. Added Lee version 2021/01/07.
2020-12	9,189,326	61,086	55,981	dbVar December 2020 Release.
2020-11	9,188,212	61,086	56,089	Added Lee version 2020/08/24.
2020-10	9,188,212	59,983	55,027	October 2020 Release.
2020-09	9,188,212	59,983	55,144	Added DECIPHER version 2020/04/17.
2020-04	9,188,212	44,309	39,477	Added DECIPHER version 2020/02.
2020-03	9,492,707	27,334	23,611	Added gnomAD version 2019/10/04. Added 1000 Genomes version 2016/08/02.

Data Access

Study Page: NCBI Curated Common Structural Variants (nstd186).
Summary of Variant Counts: nstd186 Variant Summary.
Search dbVar: nstd186 Variants.
Data Download: ftp_manifest.
dbVar Browser: nstd186 on GRCh38 chr1.
UCSC Track Hubs: Connect to Public dbVar Hub

dbVar

Database of genomic structural variation