Summary of nstd102 (Clinical Structural Variants)
Last updated: Monday, September 18, 2023.
- Methods
- Variants Filtered
- Statistics of nstd102 Variants
- Assembly Counts
- Variant Call Types
- Variant Region Types
- Clinical Significance
- Origin
- Phenotypes
- 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" | 2,737,397 |
| has dbSNP rsid | 1 |
| type=Microsatellite | 37,416 |
| only has cytogenetic placements | 3,002 |
| type=Variation | 695 |
| type=Translocation | 91 |
| type="protein only" | 95 |
| type=fusion | 10 |
| length <50bp (potential dbSNP) | 92,654 |
| Total ClinVar RCV+Alleles Filtered | 2,886,101 |
|---|
Statistics of nstd102 Variants
The following tables reflect current nstd102 status.
Assembly Counts
Variant Call Types
Variant Region Types
Clinical Significance
| Clinical Significance | Total Variant Calls | Query |
|---|
| Uncertain significance | 31,583 | "nstd102"[study] AND "Uncertain significance"[Clinical Interpretation] |
| Pathogenic | 23,338 | "nstd102"[study] AND "Pathogenic"[Clinical Interpretation] |
| Benign | 21,840 | "nstd102"[study] AND "Benign"[Clinical Interpretation] |
| Likely benign | 5,047 | "nstd102"[study] AND "Likely benign"[Clinical Interpretation] |
| Likely pathogenic | 4,731 | "nstd102"[study] AND "Likely pathogenic"[Clinical Interpretation] |
| not provided | 1,065 | "nstd102"[study] AND "not provided"[Clinical Interpretation] |
| Benign/Likely benign | 196 | "nstd102"[study] AND "Benign/Likely benign"[Clinical Interpretation] |
| conflicting data from submitters | 180 | "nstd102"[study] AND "conflicting data from submitters"[Clinical Interpretation] |
| Conflicting interpretations of pathogenicity | 46 | "nstd102"[study] AND "Conflicting interpretations of pathogenicity"[Clinical Interpretation] |
| risk factor | 30 | "nstd102"[study] AND "risk factor"[Clinical Interpretation] |
| drug response | 25 | "nstd102"[study] AND "drug response"[Clinical Interpretation] |
| association | 21 | "nstd102"[study] AND "association"[Clinical Interpretation] |
| Pathogenic/Likely pathogenic | 17 | "nstd102"[study] AND "Pathogenic/Likely pathogenic"[Clinical Interpretation] |
| Pathogenic, low penetrance | 5 | "nstd102"[study] AND "Pathogenic, low penetrance"[Clinical Interpretation] |
| other | 2 | "nstd102"[study] AND "other"[Clinical Interpretation] |
| protective | 2 | "nstd102"[study] AND "protective"[Clinical Interpretation] |
| Affects | 1 | "nstd102"[study] AND "Affects"[Clinical Interpretation] |
| Likely pathogenic, low penetrance | 1 | "nstd102"[study] AND "Likely pathogenic, low penetrance"[Clinical Interpretation] |
| Pathogenic; other | 1 | "nstd102"[study] AND "Pathogenic; other"[Clinical Interpretation] |
| Uncertain risk allele | 1 | "nstd102"[study] AND "Uncertain risk allele"[Clinical Interpretation] |
| Uncertain significance; Pathogenic/Likely pathogenic | 1 | "nstd102"[study] AND "Uncertain significance; Pathogenic/Likely pathogenic"[Clinical Interpretation] |
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. |
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 |
|---|
| August, 2023 | ClinVarFullRelease_2023-08.xml.gz | 3,061,431 | 2,886,101 | 88,133 | 83,537 | July-August 2023 Release |
| June, 2023 | ClinVarFullRelease_2023-06.xml.gz | 2,975,570 | 2,802,014 | 87,929 | 83,332 | May/June 2023 Release |
| May, 2023 | ClinVarFullRelease_2023-05.xml.gz | 2,971,536 | 2,798,545 | 87,840 | 83,251 | May/June 2023 Release |
| 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 |
Data Access
Additional Information
