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Summary of nstd102 (Clinical Structural Variants)

Last updated: Monday, September 18, 2023.

  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


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"2,737,397
has dbSNP rsid1
only has cytogenetic placements3,002
type="protein only"95
length <50bp (potential dbSNP)92,654
Total ClinVar RCV+Alleles Filtered2,886,101

Statistics of nstd102 Variants

The following tables reflect current nstd102 status.

Assembly Counts

AssemblyVariant CallsVariant RegionsQuery
GRCh3788,08483,491"nstd102"[study] AND "GRCh37"[assembly]
GRCh3887,77283,189"nstd102"[study] AND "GRCh38"[assembly]
NCBI3521"nstd102"[study] AND "NCBI35"[assembly]

Variant Call Types

Variant Call TypeTotal Variant CallsQuery
copy number loss30,828"nstd102"[study] AND "copy number loss"[variant_type]
copy number gain29,944"nstd102"[study] AND "copy number gain"[variant_type]
deletion16,823"nstd102"[study] AND "deletion"[variant_type]
duplication8,513"nstd102"[study] AND "duplication"[variant_type]
insertion598"nstd102"[study] AND "insertion"[variant_type]
interchromosomal translocation494"nstd102"[study] AND "interchromosomal translocation"[variant_type]
delins460"nstd102"[study] AND "delins"[variant_type]
intrachromosomal translocation285"nstd102"[study] AND "intrachromosomal translocation"[variant_type]
inversion118"nstd102"[study] AND "inversion"[variant_type]
complex substitution69"nstd102"[study] AND "complex substitution"[variant_type]
tandem duplication1"nstd102"[study] AND "tandem duplication"[variant_type]

Variant Region Types

Variant Region TypeTotal Variant RegionsQuery
copy number variation82,238"nstd102"[study] AND "copy number variation"[variant_type]
insertion547"nstd102"[study] AND "insertion"[variant_type]
delins406"nstd102"[study] AND "delins"[variant_type]
complex chromosomal rearrangement244"nstd102"[study] AND "complex chromosomal rearrangement"[variant_type]
complex substitution69"nstd102"[study] AND "complex substitution"[variant_type]
inversion31"nstd102"[study] AND "inversion"[variant_type]
translocation1"nstd102"[study] AND "translocation"[variant_type]
tandem duplication1"nstd102"[study] AND "tandem duplication"[variant_type]

Clinical Significance

Clinical SignificanceTotal Variant CallsQuery
Uncertain significance31,583"nstd102"[study] AND "Uncertain significance"[Clinical Interpretation]
Pathogenic23,338"nstd102"[study] AND "Pathogenic"[Clinical Interpretation]
Benign21,840"nstd102"[study] AND "Benign"[Clinical Interpretation]
Likely benign5,047"nstd102"[study] AND "Likely benign"[Clinical Interpretation]
Likely pathogenic4,731"nstd102"[study] AND "Likely pathogenic"[Clinical Interpretation]
not provided1,065"nstd102"[study] AND "not provided"[Clinical Interpretation]
Benign/Likely benign196"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 factor30"nstd102"[study] AND "risk factor"[Clinical Interpretation]
drug response25"nstd102"[study] AND "drug response"[Clinical Interpretation]
association21"nstd102"[study] AND "association"[Clinical Interpretation]
Pathogenic/Likely pathogenic17"nstd102"[study] AND "Pathogenic/Likely pathogenic"[Clinical Interpretation]
Pathogenic, low penetrance5"nstd102"[study] AND "Pathogenic, low penetrance"[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]


OriginTotal Variant CallsQuery
germline34,074"nstd102"[study] AND "germline"[Origin]
unknown28,671"nstd102"[study] AND "unknown"[Origin]
not provided18,268"nstd102"[study] AND "not provided"[Origin]
de novo2,445"nstd102"[study] AND "de novo"[Origin]
maternal1,953"nstd102"[study] AND "maternal"[Origin]
paternal1,301"nstd102"[study] AND "paternal"[Origin]
see ClinVar for details750"nstd102"[study] AND "see ClinVar for details"[Origin]
somatic385"nstd102"[study] AND "somatic"[Origin]
inherited212"nstd102"[study] AND "inherited"[Origin]
biparental54"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]


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 provided39,228"nstd102"[study] AND "not"[Clinical Phenotype] ...
see cases23,745"nstd102"[study] AND "see"[Clinical Phenotype] ...
not specified 1,728"nstd102"[study] AND "not"[Clinical Phenotype] ...
brca1- and brca2-associated hereditary breast and ovarian cancer1,142"nstd102"[study] AND "brca1"[Clinical Phenotype] ...
duchenne muscular dystrophy 846"nstd102"[study] AND "duchenne"[Clinical Phenotype] ...
colorectal neoplasms, hereditary nonpolyposis528"nstd102"[study] AND "colorectal"[Clinical Phenotype] ...
fanconi anemia, complementation group a; fanca482"nstd102"[study] AND "fanconi"[Clinical Phenotype] ...
familial hypercholesterolemia311"nstd102"[study] AND "familial"[Clinical Phenotype] ...
neurofibromatosis, type i; nf1297"nstd102"[study] AND "neurofibromatosis"[Clinical Phenotype] ...
schizophrenia; sczd228"nstd102"[study] AND "schizophrenia"[Clinical Phenotype] ...
normal pregnancy224"nstd102"[study] AND "normal"[Clinical Phenotype] ...
premature ovarian failure 1; pof1222"nstd102"[study] AND "premature"[Clinical Phenotype] ...
lynch syndrome219"nstd102"[study] AND "lynch"[Clinical Phenotype] ...
ductal breast carcinoma 218"nstd102"[study] AND "ductal"[Clinical Phenotype] ...
ataxia-telangiectasia; at214"nstd102"[study] AND "ataxia"[Clinical Phenotype] ...
early infantile epileptic encephalopathy213"nstd102"[study] AND "early"[Clinical Phenotype] ...
ciliary dyskinesia178"nstd102"[study] AND "ciliary"[Clinical Phenotype] ...
abnormal esophagus morphology165"nstd102"[study] AND "abnormal"[Clinical Phenotype] ...
cohen syndrome; coh1159"nstd102"[study] AND "cohen"[Clinical Phenotype] ...
gestational diabetes mellitus uncontrolled156"nstd102"[study] AND "gestational"[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

nstd102 Load History

Date UpdatedData SourceTotal ClinVar IDsClinVar RCV+AlleleIDs Filterednstd102 Variant Calls (Generated from ClinVar RCV+AlleleIDs)nstd102 Variant RegionsComment
August, 2023ClinVarFullRelease_2023-08.xml.gz3,061,4312,886,10188,13383,537July-August 2023 Release
June, 2023ClinVarFullRelease_2023-06.xml.gz2,975,5702,802,01487,92983,332May/June 2023 Release
May, 2023ClinVarFullRelease_2023-05.xml.gz2,971,5362,798,54587,84083,251May/June 2023 Release
April, 2023ClinVarFullRelease_2023-04.xml.gz2,927,2962,755,31687,71983,130March/April 2023 Release
March, 2023ClinVarFullRelease_2023-03.xml.gz2,901,5392,729,19188,74083,952dbVar March/April 2023 Release

Data Access

Additional Information

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Last updated: 2023-09-18T14:00:07Z