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Summary of nstd102 (Clinical Structural Variants)

Last updated: Friday, September 16, 2022.

  1. Methods
    1. Variants Filtered
  2. Statistics of nstd102 Variants
    1. Assembly Counts
    2. Variant Call Types
    3. Variant Region Types
    4. Clinical Significance
    5. Origin
    6. Phenotypes
  3. Mapping to other dbVar Studies
  4. nstd102 Load History
  5. Data Access
  6. 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 CriteriaNumber of ClinVar RCV+AlleleIDs filtered
type="single nucleotide variant"1,811,498
has dbSNP rsid1
type=Microsatellite30,148
only has cytogenetic placements3,942
type=Variation780
type=Translocation84
type="protein only"96
type=fusion10
length <50bp (potential dbSNP)55,841
Total ClinVar RCV+Alleles Filtered1,947,253

Statistics of nstd102 Variants

The following tables reflect current nstd102 status.

Assembly Counts

AssemblyVariant CallsVariant RegionsQuery
GRCh3779,18375,194"nstd102"[study] AND "GRCh37"[assembly]
GRCh3878,88674,908"nstd102"[study] AND "GRCh38"[assembly]
NCBI3521"nstd102"[study] AND "NCBI35"[assembly]

Variant Call Types

Variant Call TypeTotal Variant CallsQuery
copy number loss29,422"nstd102"[study] AND "copy number loss"[variant_type]
copy number gain28,656"nstd102"[study] AND "copy number gain"[variant_type]
deletion13,200"nstd102"[study] AND "deletion"[variant_type]
duplication6,290"nstd102"[study] AND "duplication"[variant_type]
interchromosomal translocation494"nstd102"[study] AND "interchromosomal translocation"[variant_type]
insertion432"nstd102"[study] AND "insertion"[variant_type]
intrachromosomal translocation285"nstd102"[study] AND "intrachromosomal translocation"[variant_type]
delins280"nstd102"[study] AND "delins"[variant_type]
inversion112"nstd102"[study] AND "inversion"[variant_type]
complex substitution58"nstd102"[study] AND "complex substitution"[variant_type]
tandem duplication1"nstd102"[study] AND "tandem duplication"[variant_type]
Total79,230

Variant Region Types

Variant Region TypeTotal Variant RegionsQuery
copy number variation74,246"nstd102"[study] AND "copy number variation"[variant_type]
insertion395"nstd102"[study] AND "insertion"[variant_type]
delins269"nstd102"[study] AND "delins"[variant_type]
complex chromosomal rearrangement244"nstd102"[study] AND "complex chromosomal rearrangement"[variant_type]
complex substitution58"nstd102"[study] AND "complex substitution"[variant_type]
inversion25"nstd102"[study] AND "inversion"[variant_type]
translocation1"nstd102"[study] AND "translocation"[variant_type]
tandem duplication1"nstd102"[study] AND "tandem duplication"[variant_type]
Total75,239

Clinical Significance

Clinical SignificanceTotal Variant CallsQuery
Uncertain significance26,985"nstd102"[study] AND "Uncertain significance"[Clinical Interpretation]
Benign21,818"nstd102"[study] AND "Benign"[Clinical Interpretation]
Pathogenic19,998"nstd102"[study] AND "Pathogenic"[Clinical Interpretation]
Likely benign4,986"nstd102"[study] AND "Likely benign"[Clinical Interpretation]
Likely pathogenic3,918"nstd102"[study] AND "Likely pathogenic"[Clinical Interpretation]
not provided1,011"nstd102"[study] AND "not provided"[Clinical Interpretation]
Benign/Likely benign195"nstd102"[study] AND "Benign/Likely benign"[Clinical Interpretation]
conflicting data from submitters180"nstd102"[study] AND "conflicting data from submitters"[Clinical Interpretation]
Conflicting interpretations of pathogenicity46"nstd102"[study] AND "Conflicting interpretations of pathogenicity"[Clinical Interpretation]
risk factor29"nstd102"[study] AND "risk factor"[Clinical Interpretation]
drug response25"nstd102"[study] AND "drug response"[Clinical Interpretation]
Pathogenic/Likely pathogenic17"nstd102"[study] AND "Pathogenic/Likely pathogenic"[Clinical Interpretation]
association13"nstd102"[study] AND "association"[Clinical Interpretation]
other2"nstd102"[study] AND "other"[Clinical Interpretation]
protective2"nstd102"[study] AND "protective"[Clinical Interpretation]
Affects1"nstd102"[study] AND "Affects"[Clinical Interpretation]
Likely pathogenic, low penetrance1"nstd102"[study] AND "Likely pathogenic, low penetrance"[Clinical Interpretation]
Pathogenic; other1"nstd102"[study] AND "Pathogenic; other"[Clinical Interpretation]
Uncertain risk allele1"nstd102"[study] AND "Uncertain risk allele"[Clinical Interpretation]
Uncertain significance; Pathogenic/Likely pathogenic1"nstd102"[study] AND "Uncertain significance; Pathogenic/Likely pathogenic"[Clinical Interpretation]

Origin

OriginTotal Variant CallsQuery
germline28,265"nstd102"[study] AND "germline"[Origin]
unknown25,902"nstd102"[study] AND "unknown"[Origin]
not provided18,273"nstd102"[study] AND "not provided"[Origin]
de novo2,346"nstd102"[study] AND "de novo"[Origin]
maternal1,910"nstd102"[study] AND "maternal"[Origin]
paternal1,266"nstd102"[study] AND "paternal"[Origin]
see ClinVar for details725"nstd102"[study] AND "see ClinVar for details"[Origin]
somatic281"nstd102"[study] AND "somatic"[Origin]
inherited199"nstd102"[study] AND "inherited"[Origin]
biparental43"nstd102"[study] AND "biparental"[Origin]
tested-inconclusive18"nstd102"[study] AND "tested-inconclusive"[Origin]
not applicable1"nstd102"[study] AND "not applicable"[Origin]
not-reported1"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.
PhenotypeTotal Variant CallsQuery
not provided34,904"nstd102"[study] AND "not"[Clinical Phenotype] ...
see cases23,506"nstd102"[study] AND "see"[Clinical Phenotype] ...
not specified 1,584"nstd102"[study] AND "not"[Clinical Phenotype] ...
brca1- and brca2-associated hereditary breast and ovarian cancer1,019"nstd102"[study] AND "brca1"[Clinical Phenotype] ...
duchenne muscular dystrophy 736"nstd102"[study] AND "duchenne"[Clinical Phenotype] ...
colorectal neoplasms, hereditary nonpolyposis480"nstd102"[study] AND "colorectal"[Clinical Phenotype] ...
fanconi anemia, complementation group a; fanca456"nstd102"[study] AND "fanconi"[Clinical Phenotype] ...
familial hypercholesterolemia297"nstd102"[study] AND "familial"[Clinical Phenotype] ...
neurofibromatosis, type i; nf1256"nstd102"[study] AND "neurofibromatosis"[Clinical Phenotype] ...
normal pregnancy224"nstd102"[study] AND "normal"[Clinical Phenotype] ...
premature ovarian failure 1; pof1222"nstd102"[study] AND "premature"[Clinical Phenotype] ...
ductal breast carcinoma 218"nstd102"[study] AND "ductal"[Clinical Phenotype] ...
lynch syndrome218"nstd102"[study] AND "lynch"[Clinical Phenotype] ...
ataxia-telangiectasia; at198"nstd102"[study] AND "ataxia"[Clinical Phenotype] ...
schizophrenia; sczd181"nstd102"[study] AND "schizophrenia"[Clinical Phenotype] ...
abnormal esophagus morphology165"nstd102"[study] AND "abnormal"[Clinical Phenotype] ...
early infantile epileptic encephalopathy165"nstd102"[study] AND "early"[Clinical Phenotype] ...
abnormal facial shape158"nstd102"[study] AND "abnormal"[Clinical Phenotype] ...
gestational diabetes mellitus uncontrolled156"nstd102"[study] AND "gestational"[Clinical Phenotype] ...
preeclampsia/eclampsia 1; pee1139"nstd102"[study] AND "preeclampsia"[Clinical Phenotype] ...

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:
PropertySunsetted studiesnstd102
basis of variant call identityClinVar SCVs (submitted variants)ClinVar RCV + AlleleID
experimentMultiple experimentsSingle experiment
laboratory, method, sample, subjectAssociated with each variant callNot 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, originSingle value for each variant callVariant calls are aggregated and may combine multiple and even conflicting values. Individual values can be explored by following the variant's link to ClinVar.
StudyObsolete Calls matched to nstd102Obsolete Calls not matched to nstd102
Miller et al. 201033,0357,934
User submitted curated variants22812
Kaminsky et al. 20113,787844
LSDB submitted variants1300
Ansari et al. 2016120
Blanco-Kelly et al. 201780
Total37,2008,790

nstd102 Load History

Date UpdatedData SourceTotal ClinVar IDsClinVar RCV+AlleleIDs Filterednstd102 Variant Calls (Generated from ClinVar RCV+AlleleIDs)nstd102 Variant RegionsComment
August, 2022ClinVarFullRelease_2022-08.xml.gz2,077,0311,947,25379,23075,239August 2022 Release
July, 2022ClinVarFullRelease_2022-07.xml.gz2,068,1471,939,08379,14875,163July 2022 Release
June, 2022ClinVarFullRelease_2022-06.xml.gz2,058,5101,930,10179,11675,131June 2022 Release
May, 2022ClinVarFullRelease_2022-05.xml.gz2,045,7071,918,43178,92774,957May 2022 Release
April, 2022ClinVarFullRelease_2022-04.xml.gz1,875,3081,753,44980,69376,027April 2022 Release
February, 2022ClinVarFullRelease_2022-02.xml.gz1,650,4321,553,25171,70968,808February 2022 Release
January, 2022ClinVarFullRelease_2021-12.xml.gz1,628,4001,533,11571,47468,581December 2021 Release
November, 2021ClinVarFullRelease_2021-11.xml.gz1,600,9161,491,27471,57568,675November 2021 Release
October, 2021ClinVarFullRelease_2021-10.xml.gz1,594,2061,383,56171,40668,621October 2021 Release
September, 2021ClinVarFullRelease_2021-09.xml.gz1,479,1971,383,56171,40668,522September 2021 Release
August, 2021ClinVarFullRelease_2021-08.xml.gz1,442,5771,350,02871,34068,458August 2021 Release
July, 2021ClinVarFullRelease_2021-07.xml.gz1,426,7971,336,06571,15668,294July 2021 Release
June, 2021ClinVarFullRelease_2021-06.xml.gz1,349,5381,260,65371,05268,202June 2021 Release
May, 2021ClinVarFullRelease_2021-05.xml.gz1,277,7351,195,40869,11666,511May 2021 Release
April, 2021ClinVarFullRelease_2021-04.xml.gz1,255,8401,174,38269,28966,322April 2021 Release
March, 2021ClinVarFullRelease_2021-03.xml.gz1,196,2311,119,18067,70665,250March 2021 Release
February, 2021ClinVarFullRelease_2021-02.xml.gz1,193,2331,116,73467,59165,141February 2021 Release
January, 2021ClinVarFullRelease_2021-01.xml.gz1,185,1041,109,19467,50965,062January 2021 Release
December, 2020ClinVarFullRelease_2020-12.xml.gz1,174,2791,098,84067,37364,926December 2020 Release
November, 2020ClinVarFullRelease_2020-11.xml.gz1,169,1351,094,65467,30064,856November 2020 Release
October, 2020ClinVarFullRelease_2020-10.xml.gz1,163,4711,091,37065,41962,999October 2020 Release
September, 2020ClinVarFullRelease_2020-09.xml.gz1,161,2161,089,59765,24162,827September 2020 release
August, 2020ClinVarFullRelease_2020-08.xml.gz1,169,2711,098,21465,13462,722August Release
July, 2020ClinVarFullRelease_2020-07.xml.gz1,113,5741,047,30764,89662,493July Release
June, 2020ClinVarFullRelease_2020-06.xml.gz1,089,9061,014,70464,79562,565June Release
May, 2020ClinVarFullRelease_2020-05.xml.gz1,012,185937,67664,72662,503May Release
April, 2020ClinVarFullRelease_2020-04.xml.gz956,248888,16661,61559,517April Release
February, 2020ClinVarFullRelease_2020-02.xml.gz926,091863,23859,05856,983Filtered delins, insertions, and inversions < 50bp
December, 2019ClinVarFullRelease_2019-12.xml.gz790,676731,22459,71357,597Filtered deletions and duplications < 50 bp
October 2019ClinVarFullRelease_2019-10.xml.gz786,979728,00863,15660,993
August 2019ClinVarFullRelease_2019-08.xml.gz727,082671,26559,96558,234
June 2019ClinVarFullRelease_2019-06.xml.gz718,528660,31258,85857,168
April 2019ClinVarFullRelease_2019-04.xml.gz704,243647,36857,52055,722
March 2019ClinVarFullRelease_2019-03.xml.gz696,268640,02356,92855,147Began importing variants from ClinVar XML. Preserved existing nstd102 accessions. Dropped inactive calls and and regions.

Data Access

Additional Information

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