Summary of nstd102 (Clinical Structural Variants)
Last updated: Friday, May 19, 2023.
- Methods
- Statistics of nstd102 Variants
- Mapping to other dbVar Studies
- nstd102 Load History
- Data Access
- Additional Information
Methods
nstd102 contains Structural Variants (SV) imported from ClinVar. It is intended to replace and supplement clinical variants from several studies that were originally submitted to dbVar (e.g., nstd37, nstd101). nstd102 is kept up to date with the latest ClinVar XML available on the public ClinVar FTP site. dbVar variant calls are generated from unique combinations of ClinVar RCV and Allele ID's found in the ClinVar XML, and are filtered to remove small variants as described below. The following sections summarize the statistics of various fields in the nstd102 study.
Variants Filtered
The ClinVar XML contains both large and small variants. dbVar filters out variants that meet any of the following criteria (counts reflect current nstd102 status):
| Filtering Criteria | Number of ClinVar RCV+AlleleIDs filtered |
|---|---|
| type="single nucleotide variant" | 2,607,403 |
| has dbSNP rsid | 1 |
| type=Microsatellite | 36,972 |
| only has cytogenetic placements | 3,181 |
| type=Variation | 727 |
| type=Translocation | 89 |
| type="protein only" | 95 |
| type=fusion | 10 |
| length <50bp (potential dbSNP) | 89,690 |
| Total ClinVar RCV+Alleles Filtered | 2,755,316 |
Statistics of nstd102 Variants
The following tables reflect current nstd102 status.
Assembly Counts
| Assembly | Variant Calls | Variant Regions | Query |
|---|---|---|---|
| GRCh37 | 87,670 | 83,084 | "nstd102"[study] AND "GRCh37"[assembly] |
| GRCh38 | 87,358 | 82,782 | "nstd102"[study] AND "GRCh38"[assembly] |
| NCBI35 | 2 | 1 | "nstd102"[study] AND "NCBI35"[assembly] |
Variant Call Types
| Variant Call Type | Total Variant Calls | Query |
|---|---|---|
| copy number loss | 30,685 | "nstd102"[study] AND "copy number loss"[variant_type] |
| copy number gain | 29,882 | "nstd102"[study] AND "copy number gain"[variant_type] |
| deletion | 16,676 | "nstd102"[study] AND "deletion"[variant_type] |
| duplication | 8,459 | "nstd102"[study] AND "duplication"[variant_type] |
| insertion | 598 | "nstd102"[study] AND "insertion"[variant_type] |
| interchromosomal translocation | 494 | "nstd102"[study] AND "interchromosomal translocation"[variant_type] |
| delins | 452 | "nstd102"[study] AND "delins"[variant_type] |
| intrachromosomal translocation | 285 | "nstd102"[study] AND "intrachromosomal translocation"[variant_type] |
| inversion | 118 | "nstd102"[study] AND "inversion"[variant_type] |
| complex substitution | 69 | "nstd102"[study] AND "complex substitution"[variant_type] |
| tandem duplication | 1 | "nstd102"[study] AND "tandem duplication"[variant_type] |
| Total | 87,719 |
Variant Region Types
| Variant Region Type | Total Variant Regions | Query |
|---|---|---|
| copy number variation | 81,839 | "nstd102"[study] AND "copy number variation"[variant_type] |
| insertion | 545 | "nstd102"[study] AND "insertion"[variant_type] |
| delins | 400 | "nstd102"[study] AND "delins"[variant_type] |
| complex chromosomal rearrangement | 244 | "nstd102"[study] AND "complex chromosomal rearrangement"[variant_type] |
| complex substitution | 69 | "nstd102"[study] AND "complex substitution"[variant_type] |
| inversion | 31 | "nstd102"[study] AND "inversion"[variant_type] |
| translocation | 1 | "nstd102"[study] AND "translocation"[variant_type] |
| tandem duplication | 1 | "nstd102"[study] AND "tandem duplication"[variant_type] |
| Total | 83,130 |
Clinical Significance
Origin
| Origin | Total Variant Calls | Query |
|---|---|---|
| germline | 33,796 | "nstd102"[study] AND "germline"[Origin] |
| unknown | 28,606 | "nstd102"[study] AND "unknown"[Origin] |
| not provided | 18,268 | "nstd102"[study] AND "not provided"[Origin] |
| de novo | 2,413 | "nstd102"[study] AND "de novo"[Origin] |
| maternal | 1,939 | "nstd102"[study] AND "maternal"[Origin] |
| paternal | 1,288 | "nstd102"[study] AND "paternal"[Origin] |
| see ClinVar for details | 748 | "nstd102"[study] AND "see ClinVar for details"[Origin] |
| somatic | 384 | "nstd102"[study] AND "somatic"[Origin] |
| inherited | 209 | "nstd102"[study] AND "inherited"[Origin] |
| biparental | 48 | "nstd102"[study] AND "biparental"[Origin] |
| tested-inconclusive | 18 | "nstd102"[study] AND "tested-inconclusive"[Origin] |
| not applicable | 1 | "nstd102"[study] AND "not applicable"[Origin] |
| not-reported | 1 | "nstd102"[study] AND "not-reported"[Origin] |
Phenotypes
The following table shows the 20 most frequent phenotype values for nstd102 variants.
Please note:
- The term 'not provided' is registered in MedGen to support identification of submissions to ClinVar for which no condition was named when assessing the variant. 'not provided' differs from 'not specified', which is used when a variant is asserted to be Benign, Likely benign, or of Uncertain significance for conditions that have not been specified.
- 'see cases' indicates multiple phenotypes were present in the corresponding ClinVar record. Phenotype values can be found by consulting ClinVar.
Mapping to other dbVar Studies
All clinical variants from other studies in have been re-accessioned in Clinical Structural Variants (nstd102). The studies listed in the summary table below will be sunsetted (retired) in 2021. A file mapping accessions in other studies to those in nstd102 is available at nstd102_accession_mapping.txt. Please note these differences between the sunsetted studies and nstd102:| Property | Sunsetted studies | nstd102 |
|---|---|---|
| basis of variant call identity | ClinVar SCVs (submitted variants) | ClinVar RCV + AlleleID |
| experiment | Multiple experiments | Single experiment |
| laboratory, method, sample, subject | Associated with each variant call | Not reported. Variant calls are aggregated and may combine data from multiple sources. Individual values can be explored by following the variant's link to ClinVar. |
| clinical significance, phenotype, origin | Single value for each variant call | Variant calls are aggregated and may combine multiple and even conflicting values. Individual values can be explored by following the variant's link to ClinVar. |
| Study | Obsolete Calls matched to nstd102 | Obsolete Calls not matched to nstd102 |
|---|---|---|
| Miller et al. 2010 | 33,035 | 7,934 |
| User submitted curated variants | 228 | 12 |
| Kaminsky et al. 2011 | 3,787 | 844 |
| LSDB submitted variants | 130 | 0 |
| Ansari et al. 2016 | 12 | 0 |
| Blanco-Kelly et al. 2017 | 8 | 0 |
| Total | 37,200 | 8,790 |
nstd102 Load History
| Date Updated | Data Source | Total ClinVar IDs | ClinVar RCV+AlleleIDs Filtered | nstd102 Variant Calls (Generated from ClinVar RCV+AlleleIDs) | nstd102 Variant Regions | Comment |
|---|---|---|---|---|---|---|
| April, 2023 | ClinVarFullRelease_2023-04.xml.gz | 2,927,296 | 2,755,316 | 87,719 | 83,130 | March/April 2023 Release |
| March, 2023 | ClinVarFullRelease_2023-03.xml.gz | 2,901,539 | 2,729,191 | 88,740 | 83,952 | dbVar March/April 2023 Release |
| March, 2023 | ClinVarFullRelease_2023-03.xml.gz | 2,901,539 | 2,729,191 | 88,740 | 83,952 | dbVar March/April 2023 Release |
| March, 2023 | ClinVarFullRelease_2023-03.xml.gz | 2,901,539 | 2,729,191 | 88,607 | 83,824 | dbVar March/April 2023 Release |
| February, 2023 | ClinVarFullRelease_2023-02.xml.gz | 2,879,862 | 2,714,140 | 82,840 | 78,719 | dbVar February 2023 Release |
| January, 2023 | ClinVarFullRelease_2023-01.xml.gz | 2,302,323 | 2,157,884 | 82,401 | 78,286 | dbVar January 2023 Release |
| January, 2023 | ClinVarFullRelease_2022-12.xml.gz | 2,255,157 | 2,114,689 | 80,232 | 76,176 | dbVar December 2022 Release |
| November, 2022 | ClinVarFullRelease_2022-11.xml.gz | 2,099,697 | 1,966,701 | 79,955 | 75,924 | dbVar November 2022 Release |
| October, 2022 | ClinVarFullRelease_2022-10.xml.gz | 2,091,616 | 1,959,640 | 79,768 | 75,744 | dbVar October 2022 Release |
| August, 2022 | ClinVarFullRelease_2022-08.xml.gz | 2,077,031 | 1,947,253 | 79,230 | 75,239 | August 2022 Release |
| July, 2022 | ClinVarFullRelease_2022-07.xml.gz | 2,068,147 | 1,939,083 | 79,148 | 75,163 | July 2022 Release |
| June, 2022 | ClinVarFullRelease_2022-06.xml.gz | 2,058,510 | 1,930,101 | 79,116 | 75,131 | June 2022 Release |
| May, 2022 | ClinVarFullRelease_2022-05.xml.gz | 2,045,707 | 1,918,431 | 78,927 | 74,957 | May 2022 Release |
| April, 2022 | ClinVarFullRelease_2022-04.xml.gz | 1,875,308 | 1,753,449 | 80,693 | 76,027 | April 2022 Release |
| February, 2022 | ClinVarFullRelease_2022-02.xml.gz | 1,650,432 | 1,553,251 | 71,709 | 68,808 | February 2022 Release |
| January, 2022 | ClinVarFullRelease_2021-12.xml.gz | 1,628,400 | 1,533,115 | 71,474 | 68,581 | December 2021 Release |
| November, 2021 | ClinVarFullRelease_2021-11.xml.gz | 1,600,916 | 1,491,274 | 71,575 | 68,675 | November 2021 Release |
| October, 2021 | ClinVarFullRelease_2021-10.xml.gz | 1,594,206 | 1,383,561 | 71,406 | 68,621 | October 2021 Release |
| September, 2021 | ClinVarFullRelease_2021-09.xml.gz | 1,479,197 | 1,383,561 | 71,406 | 68,522 | September 2021 Release |
| August, 2021 | ClinVarFullRelease_2021-08.xml.gz | 1,442,577 | 1,350,028 | 71,340 | 68,458 | August 2021 Release |
| July, 2021 | ClinVarFullRelease_2021-07.xml.gz | 1,426,797 | 1,336,065 | 71,156 | 68,294 | July 2021 Release |
| June, 2021 | ClinVarFullRelease_2021-06.xml.gz | 1,349,538 | 1,260,653 | 71,052 | 68,202 | June 2021 Release |
| May, 2021 | ClinVarFullRelease_2021-05.xml.gz | 1,277,735 | 1,195,408 | 69,116 | 66,511 | May 2021 Release |
| April, 2021 | ClinVarFullRelease_2021-04.xml.gz | 1,255,840 | 1,174,382 | 69,289 | 66,322 | April 2021 Release |
| March, 2021 | ClinVarFullRelease_2021-03.xml.gz | 1,196,231 | 1,119,180 | 67,706 | 65,250 | March 2021 Release |
| February, 2021 | ClinVarFullRelease_2021-02.xml.gz | 1,193,233 | 1,116,734 | 67,591 | 65,141 | February 2021 Release |
| January, 2021 | ClinVarFullRelease_2021-01.xml.gz | 1,185,104 | 1,109,194 | 67,509 | 65,062 | January 2021 Release |
| December, 2020 | ClinVarFullRelease_2020-12.xml.gz | 1,174,279 | 1,098,840 | 67,373 | 64,926 | December 2020 Release |
| November, 2020 | ClinVarFullRelease_2020-11.xml.gz | 1,169,135 | 1,094,654 | 67,300 | 64,856 | November 2020 Release |
| October, 2020 | ClinVarFullRelease_2020-10.xml.gz | 1,163,471 | 1,091,370 | 65,419 | 62,999 | October 2020 Release |
| September, 2020 | ClinVarFullRelease_2020-09.xml.gz | 1,161,216 | 1,089,597 | 65,241 | 62,827 | September 2020 release |
| August, 2020 | ClinVarFullRelease_2020-08.xml.gz | 1,169,271 | 1,098,214 | 65,134 | 62,722 | August Release |
| July, 2020 | ClinVarFullRelease_2020-07.xml.gz | 1,113,574 | 1,047,307 | 64,896 | 62,493 | July Release |
| June, 2020 | ClinVarFullRelease_2020-06.xml.gz | 1,089,906 | 1,014,704 | 64,795 | 62,565 | June Release |
| May, 2020 | ClinVarFullRelease_2020-05.xml.gz | 1,012,185 | 937,676 | 64,726 | 62,503 | May Release |
| April, 2020 | ClinVarFullRelease_2020-04.xml.gz | 956,248 | 888,166 | 61,615 | 59,517 | April Release |
| February, 2020 | ClinVarFullRelease_2020-02.xml.gz | 926,091 | 863,238 | 59,058 | 56,983 | Filtered delins, insertions, and inversions < 50bp |
| December, 2019 | ClinVarFullRelease_2019-12.xml.gz | 790,676 | 731,224 | 59,713 | 57,597 | Filtered deletions and duplications < 50 bp |
| October 2019 | ClinVarFullRelease_2019-10.xml.gz | 786,979 | 728,008 | 63,156 | 60,993 | |
| August 2019 | ClinVarFullRelease_2019-08.xml.gz | 727,082 | 671,265 | 59,965 | 58,234 | |
| June 2019 | ClinVarFullRelease_2019-06.xml.gz | 718,528 | 660,312 | 58,858 | 57,168 | |
| April 2019 | ClinVarFullRelease_2019-04.xml.gz | 704,243 | 647,368 | 57,520 | 55,722 | |
| March 2019 | ClinVarFullRelease_2019-03.xml.gz | 696,268 | 640,023 | 56,928 | 55,147 | Began importing variants from ClinVar XML. Preserved existing nstd102 accessions. Dropped inactive calls and and regions. |
Data Access
- Study Page: Clinical Structural Variants (nstd102).
- Summary of Variant Counts: nstd102 Variant Summary.
- Search dbVar: nstd102 Variants.
- Data Download: ftp_manifest.
- dbVar Browser: nstd102 on GRCh38 chr1.
- UCSC Track Hubs: Connect to Public dbVar Hub