Summary of nstd102 (Clinical Structural Variants)

Last updated: Thursday, March 25, 2021.

  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, etc.). 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 describe the mapping between nstd102 and variants in other dbVar studies, and 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"1,022,213
has dbSNP rsid90,790
type=Microsatellite16,103
only has cytogenetic placements4,517
type=Variation743
type=Translocation256
type="protein only"99
type=fusion10
length <50bp (potential dbSNP)13,635
Total ClinVar RCV+Alleles Filtered1,119,180

Statistics of nstd102 Variants

The following tables reflect current nstd102 status.

Assembly Counts

AssemblyVariant CallsVariant RegionsQuery
GRCh3767,53465,091"nstd102"[study] AND "GRCh37"[assembly]
GRCh3867,22464,794"nstd102"[study] AND "GRCh38"[assembly]

Variant Call Types

Variant Call TypeTotal Variant CallsQuery
copy number loss28,559"nstd102"[study] AND "copy number loss"[variant_type]
copy number gain27,973"nstd102"[study] AND "copy number gain"[variant_type]
deletion7,456"nstd102"[study] AND "deletion"[variant_type]
duplication3,154"nstd102"[study] AND "duplication"[variant_type]
delins220"nstd102"[study] AND "delins"[variant_type]
insertion154"nstd102"[study] AND "insertion"[variant_type]
complex substitution54"nstd102"[study] AND "complex substitution"[variant_type]
inversion18"nstd102"[study] AND "inversion"[variant_type]
tandem duplication1"nstd102"[study] AND "tandem duplication"[variant_type]
Total67,589

Variant Region Types

Variant Region TypeTotal Variant RegionsQuery
copy number variation64,720"nstd102"[study] AND "copy number variation"[variant_type]
delins209"nstd102"[study] AND "delins"[variant_type]
insertion139"nstd102"[study] AND "insertion"[variant_type]
complex substitution54"nstd102"[study] AND "complex substitution"[variant_type]
inversion18"nstd102"[study] AND "inversion"[variant_type]
tandem duplication1"nstd102"[study] AND "tandem duplication"[variant_type]
Total65,141

Clinical Significance

Clinical SignificanceTotal Variant CallsQuery
Uncertain significance21,813"nstd102"[study] AND "Uncertain significance"[Clinical Interpretation]
Benign21,751"nstd102"[study] AND "Benign"[Clinical Interpretation]
Pathogenic15,160"nstd102"[study] AND "Pathogenic"[Clinical Interpretation]
Likely benign4,823"nstd102"[study] AND "Likely benign"[Clinical Interpretation]
Likely pathogenic2,614"nstd102"[study] AND "Likely pathogenic"[Clinical Interpretation]
not provided916"nstd102"[study] AND "not provided"[Clinical Interpretation]
Benign/Likely benign196"nstd102"[study] AND "Benign/Likely benign"[Clinical Interpretation]
conflicting data from submitters193"nstd102"[study] AND "conflicting data from submitters"[Clinical Interpretation]
Conflicting interpretations of pathogenicity46"nstd102"[study] AND "Conflicting interpretations of pathogenicity"[Clinical Interpretation]
drug response25"nstd102"[study] AND "drug response"[Clinical Interpretation]
Pathogenic/Likely pathogenic20"nstd102"[study] AND "Pathogenic/Likely pathogenic"[Clinical Interpretation]
risk factor17"nstd102"[study] AND "risk factor"[Clinical Interpretation]
association11"nstd102"[study] AND "association"[Clinical Interpretation]
protective2"nstd102"[study] AND "protective"[Clinical Interpretation]
Affects1"nstd102"[study] AND "Affects"[Clinical Interpretation]
other1"nstd102"[study] AND "other"[Clinical Interpretation]

Origin

OriginTotal Variant CallsQuery
unknown25,183"nstd102"[study] AND "unknown"[Origin]
not provided20,144"nstd102"[study] AND "not provided"[Origin]
germline16,586"nstd102"[study] AND "germline"[Origin]
maternal1,854"nstd102"[study] AND "maternal"[Origin]
de novo1,461"nstd102"[study] AND "de novo"[Origin]
paternal1,211"nstd102"[study] AND "paternal"[Origin]
see ClinVar for details709"nstd102"[study] AND "see ClinVar for details"[Origin]
somatic275"nstd102"[study] AND "somatic"[Origin]
inherited107"nstd102"[study] AND "inherited"[Origin]
biparental40"nstd102"[study] AND "biparental"[Origin]
tested-inconclusive18"nstd102"[study] AND "tested-inconclusive"[Origin]
not applicable1"nstd102"[study] AND "not applicable"[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 provided30,827"nstd102"[study] AND "not"[Clinical Phenotype] ...
see cases25,325"nstd102"[study] AND "see"[Clinical Phenotype] ...
brca1- and brca2-associated hereditary breast and ovarian cancer740"nstd102"[study] AND "brca1"[Clinical Phenotype] ...
duchenne muscular dystrophy 435"nstd102"[study] AND "duchenne"[Clinical Phenotype] ...
46,xy disorder of sexual development due to dihydrotestosterone backdoor pathway biosynthesis defect302"nstd102"[study] AND "xy"[Clinical Phenotype] ...
familial hypercholesterolemia255"nstd102"[study] AND "familial"[Clinical Phenotype] ...
fanconi anemia, complementation group a; fanca254"nstd102"[study] AND "fanconi"[Clinical Phenotype] ...
colorectal cancer, hereditary nonpolyposis225"nstd102"[study] AND "colorectal"[Clinical Phenotype] ...
normal pregnancy224"nstd102"[study] AND "normal"[Clinical Phenotype] ...
premature ovarian failure 1; pof1221"nstd102"[study] AND "premature"[Clinical Phenotype] ...
ductal breast carcinoma 218"nstd102"[study] AND "ductal"[Clinical Phenotype] ...
schizophrenia; sczd179"nstd102"[study] AND "schizophrenia"[Clinical Phenotype] ...
neurofibromatosis, type i; nf1167"nstd102"[study] AND "neurofibromatosis"[Clinical Phenotype] ...
abnormal esophagus morphology165"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] ...
large for gestational age121"nstd102"[study] AND "large"[Clinical Phenotype] ...
not specified 121"nstd102"[study] AND "not"[Clinical Phenotype] ...
small for gestational age116"nstd102"[study] AND "small"[Clinical Phenotype] ...
ataxia-telangiectasia; at114"nstd102"[study] AND "ataxia"[Clinical Phenotype] ...

Mapping to other dbVar Studies

All clinical variants from other studies in have been re-accessioned in Clinical Structural Variants (nstd102) . The nstd102 accessions are preferred and will be kept up to date with changes made in ClinVar. We recommend using the nstd102 accessions whenever possible. A file mapping accessions in other studies to those in nstd102 is available at nstd102_accession_mapping.txt .

Please note:

  • nstd102 variant calls are based on ClinVar RCV+AlleleID.
  • Previous variant calls in nstd102 were based on ClinVar RCVs.
  • Variant calls in other studies, such as nstd37 and nstd101, are based on ClinVar SCVs (submitted variants).
  • nstd102 contains a single experiment with method=Multiple and analysis=Multiple.
  • nstd102 does not identify submitting laboratories as do nstd37 and nstd101.
  • nstd102 variant calls may combine submitted variants from both nstd37 and nstd101.
  • nstd102 variant calls may combine submitted variants from multiple submitters.
  • nstd102 variant calls may combine submitted variants from multiple methods.
  • nstd102 variant calls may combine submitted variants from multiple subjects.
  • nstd102 variant calls are not linked directly to samples and subjects as are the calls in nstd37 and nstd101.
  • nstd102 variant calls are less-specific than calls in other studies, and may contain multiple or conflicting values of clinical significance, phenotype, and origin.
  • Some nstd37 and nstd101 variants are not mapped to nstd102 because they were not submitted to ClinVar due to copy_number warnings.
  • Some nstd51 and nstd133 variants are not mapped to nstd102 because they were initially submitted to ClinVar with cytogenetic placements, and to dbVar with genomic placements.
  • Some nstd133 calls are not mapped to nstd102 because they are Translocations, which have not been imported from ClinVar to nstd102.
StudyCalls matched to nstd102Calls not matched to nstd102Matching nstd102 calls
Miller et al. 201033,01236620,913
User submitted curated variants20921225
Kaminsky et al. 20113,785483,154
LSDB submitted variants1291135
Redin et al. 201609210
Kasak et al. 201508790
Ansari et al. 201612011
Blanco-Kelly et al. 2017080
Total37,1472,24424,438

nstd102 Load History

Date UpdatedData SourceTotal ClinVar IDsClinVar RCV+AlleleIDs Filterednstd102 Variant Calls (Generated from ClinVar RCV+AlleleIDs)nstd102 Variant RegionsComment
March, 2021ClinVarFullRelease_2021-03.xml.gz1,196,2311,119,18067,70665,250March 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

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Last updated: 2021-03-25T16:59:12Z