Schema for ClinVar Variants - ClinVar Variants
  Database: hg38    Primary Table: clinvarCnv Data last updated: 2020-06-17
Big Bed File: /gbdb/hg38/bbi/clinvarCnv.bb
Item Count: 19,500
Format description: Browser extensible data (12 fields) plus information about a ClinVar entry. _clinSignCode has these possible values: BN=benign, LB=likely benign, CF=conflicting, PG=pathogenic, LP=likely pathogenic, UC=uncertain, OT=other
fieldexampledescription
chromchr1Chromosome (or contig, scaffold, etc.)
chromStart149854268Start position in chromosome
chromEnd180267197End position in chromosome
name1q21.2-25.2Name of item
score0Score from 0-1000
strand.+ or -
thickStart149854268Start of where display should be thick (start codon)
thickEnd180267197End of where display should be thick (stop codon)
reserved17,44,138Used as itemRgb as of 2004-11-22
blockCount1Number of blocks
blockSizes30412929Comma separated list of block sizes
chromStarts0Start positions relative to chromStart
origName155448|GRCh38/hg38 1q21.2-25.2(chr1:149854269-180267197)x3Link to ClinVar
clinSignPathogenicClinical significance
reviewStatus☆☆☆☆  based on: no assertion criteria providedReview Status
typecopy number gainType of Variant
geneIdsubset of 664 genes:ASH1L,FLG,GATAD2B,LHX4,LMNA,PBX1,POGZ,SDHC,SF3B4Gene Symbol
molConseqMolecular Consequence
snpIddbSNP ID
nsvIdnsv995575dbVar ID
rcvAccRCV000143515ClinVar Allele Submission
testedInGtrNGenetic Testing Registry
phenotypeListSee casesPhenotypes
phenotypenaPhenotype identifiers
originnot providedAllele origin
assemblyGRCh38Genome assembly
cytogenetic1q21.2-25.2Cytogenetic status
hgvsCodNucleotide HGVS
hgvsProtProtein HGVS
numSubmit1Number of submitters
lastEvalJul 16,2013Last evaluation
guidelinesGuidelines
otherIdsdbVar:nssv3397176, dbVar:nsv995575Other identifiers e.g. OMIM IDs, etc.
_mouseOverGRCh38/hg38 1q21.2-25.2(chr1:149854269-180267197)x3, Type: copy number gain, Consequence: , Significance: Pathogenic, Origin: not provided, Phenotypes: See casesMouse over text
_clinSignCodePGClinical Significance
_originCodeUNKAllele Origin Code
_allTypeCodeDUPLVariation Type
_varLen30412929Variant Length in base pairs
_starCount0 number of stars

Sample Rows
 
chromchromStartchromEndnamescorestrandthickStartthickEndreservedblockCountblockSizeschromStartsorigNameclinSignreviewStatustypegeneIdmolConseqsnpIdnsvIdrcvAcctestedInGtrphenotypeListphenotypeoriginassemblycytogenetichgvsCodhgvsProtnumSubmitlastEvalguidelinesotherIds_mouseOver_clinSignCode_originCode_allTypeCode_varLen_starCount
chr11498542681802671971q21.2-25.20.14985426818026719717,44,1381304129290155448|GRCh38/hg38 1q21.2-25.2(chr1:149854269-180267197)x3Pathogenic☆☆☆☆  based on: no assertion criteria providedcopy number gainsubset of 664 genes:ASH1L,FLG,GATAD2B,LHX4,LMNA,PBX1,POGZ,SDHC,SF3B4nsv995575RCV000143515NSee casesnanot providedGRCh381q21.2-25.21Jul 16,2013dbVar:nssv3397176, ...GRCh38/hg38 1q21.2-25.2(chr1:149854269-180267197)x3, Type: copy number gain, Consequence: , Significance: Pathogenic, Origin: no ...PGUNKDUPL304129290
chr11577472451760212471q23.1-25.11.15774724517602124717,44,138118274002058109|GRCh38/hg38 1q23.1-25.1(chr1:157747246-176021247)x3Pathogenic★☆☆☆  based on: criteria provided,single submittercopy number gainsubset of 326 genes:PBX1,SDHCnsv530567RCV000051854NSee casesnanot providedGRCh381q23.1-25.11Aug 12,2011dbVar:nssv578535, ...GRCh38/hg38 1q23.1-25.1(chr1:157747246-176021247)x3, Type: copy number gain, Consequence: , Significance: Pathogenic, Origin: no ...PGUNKDUPL182740021
chr11594798861668950861q23.2-24.11.159479886166895086180,3,1617415200057465|GRCh38/hg38 1q23.2-24.1(chr1:159479887-166895086)x1Pathogenic★☆☆☆  based on: criteria provided,single submittercopy number losssubset of 159 genes:PBX1,SDHCnsv529716RCV000051172NSee casesnanot providedGRCh381q23.2-24.11Aug 12,2011dbVar:nssv577227, ...GRCh38/hg38 1q23.2-24.1(chr1:159479887-166895086)x1, Type: copy number loss, Consequence: , Significance: Pathogenic, Origin: no ...PGUNKDEL74152001
chr11617409061739651541q23.3-25.11.161740906173965154180,3,16112224248060042|GRCh38/hg38 1q23.3-25.1(chr1:161740907-173965154)x1Pathogenic★☆☆☆  based on: criteria provided,single submittercopy number losssubset of 158 genes:PBX1nsv532581RCV000053914NSee casesnade novoGRCh381q23.3-25.11Aug 12,2011dbVar:nssv577229, ...GRCh38/hg38 1q23.3-25.1(chr1:161740907-173965154)x1, Type: copy number loss, Consequence: , Significance: Pathogenic, Origin: de ...PGGERMDEL122242481
chr11620400491674806631q23.3-24.21.162040049167480663180,3,1615440614060043|GRCh38/hg38 1q23.3-24.2(chr1:162040050-167480663)x1Pathogenic★☆☆☆  based on: criteria provided,single submittercopy number losssubset of 54 genes:PBX1nsv532582RCV000053915NSee casesnanot providedGRCh381q23.3-24.21Aug 12,2011dbVar:nssv577230, ...GRCh38/hg38 1q23.3-24.2(chr1:162040050-167480663)x1, Type: copy number loss, Consequence: , Significance: Pathogenic, Origin: no ...PGUNKDEL54406141
chr11633825221758770221q23.3-25.10.163382522175877022180,3,161124945000155225|GRCh38/hg38 1q23.3-25.1(chr1:163382523-175877022)x1Pathogenic☆☆☆☆  based on: no assertion criteria providedcopy number losssubset of 149 genes:PBX1nsv932260RCV000143292NSee casesnanot providedGRCh381q23.3-25.11Mar 19,2013dbVar:nssv1610454, ...GRCh38/hg38 1q23.3-25.1(chr1:163382523-175877022)x1, Type: copy number loss, Consequence: , Significance: Pathogenic, Origin: no ...PGUNKDEL124945000
chr11649226541800615891q23.3-25.21.16492265418006158917,44,138115138935058111|GRCh38/hg38 1q23.3-25.2(chr1:164922655-180061589)x3Pathogenic★☆☆☆  based on: criteria provided,single submittercopy number gaincovers 174 genes,none of which curated to show dosage sensitivitynsv530569RCV000051856NSee casesnanot providedGRCh381q23.3-25.21Aug 12,2011dbVar:nssv578537, ...GRCh38/hg38 1q23.3-25.2(chr1:164922655-180061589)x3, Type: copy number gain, Consequence: , Significance: Pathogenic, Origin: no ...PGUNKDUPL151389351
chr11660315451669792761q24.10.166031545166979276208,50,6019477310150235|GRCh38/hg38 1q24.1(chr1:166031546-166979276)x1Uncertain significance☆☆☆☆  based on: no assertion criteria providedcopy number lossFAM78B,FAM78B-AS1,ILDR2,LINC01675,LOC113939980,MAEL,MIR921,POGK,TADA1nsv916491RCV000139120NSee casesnanot providedGRCh381q24.11Jul 09,2012dbVar:nssv1602726, ...GRCh38/hg38 1q24.1(chr1:166031546-166979276)x1, Type: copy number loss, Consequence: , Significance: Uncertain significance, Ori ...UCUNKDEL9477310
chr11667628311753274231q24.1-25.11.166762831175327423180,3,1618564592060045|GRCh38/hg38 1q24.1-25.1(chr1:166762832-175327423)x1Pathogenic★☆☆☆  based on: criteria provided,single submittercopy number losscovers 123 genes,none of which curated to show dosage sensitivitynsv532584RCV000053917NSee casesnade novoGRCh381q24.1-25.11Aug 12,2011dbVar:nssv577232, ...GRCh38/hg38 1q24.1-25.1(chr1:166762832-175327423)x1, Type: copy number loss, Consequence: , Significance: Pathogenic, Origin: de ...PGGERMDEL85645921
chr11678010651678630281q24.20.167801065167863028227,142,1441619630151438|GRCh38/hg38 1q24.2(chr1:167801066-167863028)x1Likely benign☆☆☆☆  based on: no assertion criteria providedcopy number loss55811|ADCY10nsv931324RCV000140151NSee casesnanot providedGRCh381q24.21Apr 30,2011dbVar:nssv1609232, ...GRCh38/hg38 1q24.2(chr1:167801066-167863028)x1, Type: copy number loss, Consequence: , Significance: Likely benign, Origin: not ...LBUNKDEL619630

ClinVar Variants (clinvar) Track Description
 

Description

NOTE:
ClinVar is intended for use primarily by physicians and other professionals concerned with genetic disorders, by genetics researchers, and by advanced students in science and medicine. While the ClinVar database is open to all academic users, users seeking information about a personal medical or genetic condition are urged to consult with a qualified physician for diagnosis and for answers to personal questions.

This track shows the genomic positions of variants in the ClinVar database. ClinVar is a free, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence. The track is updated after every ClinVar release, once a month.

Note: The data in the track are obtained directly from ClinVar's FTP site. We display the data obtained from ClinVar as-is to avoid discrepancies between UCSC and NCBI. However, be aware that the ClinVar conventions are different from the VCF standard. Variants may be right-aligned or may contain additional context, e.g. for inserts. ExAC/gnomAD make available a converter to make ClinVar more comparable to VCF files.

Display Conventions and Configuration

Genomic locations of ClinVar variants are labeled with the ClinVar variant descriptions. All information related to each is variant is shown on that variant's details page. Leave the mouse over a feature for more than 2 seconds to show the clinical significance of a variant.

The track is divided into two subtracks, one for copy number variants (CNVs), which are all variants longer than 100bp, and a second track for shorter substitutions and indels.

Until October 2017, all variants with the ClinVar types copy number gain/loss and DbVar "nsv" accessions were put in the CNV category. Due to the ClinVar type not capturing this information anymore, anything longer than 100bp is now considered a CNV.

Entries in the ClinVar CNV track are colored red for loss and blue for gain.

Entries in the ClinVar short variants track are shaded by clinical annotation: red for pathogenic, dark grey for uncertain significance or not provided and green for benign.

The score of the variants is the number of "stars" in ClinVar. On the track configuration page (above), you can filter the track to show only variants with more than a certain number of stars. For more information on the star rating, see the ClinVar documentation.

Data updates

ClinVar publishes a new release on the first Thursday every month and this track is updated automatically at most six days later. The exact date of our last update is shown when you click onto any variant. You can find the previous versions of the track organized by month on our downloads server in the archive directory. To access one of these previous versions, paste the URL to one of the older files into our "Custom tracks" box.

Data access

The raw data can be explored interactively with the Table Browser or the Data Integrator.

For automated download and analysis, the genome annotation is stored in a bigBed file that can be downloaded from our download server. The files for this track are called clinVarMain.bb and clinVarCnv.bb. Individual regions or the whole genome annotation can be obtained using our tool bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tool can also be used to obtain only features within a given range, e.g. bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg19/bbi/clinvar/clinvarMain.bb -chrom=chr21 -start=0 -end=100000000 stdout

Methods

ClinVar files were reformatted at UCSC to the bigBed format. The data is updated every month, one week after the ClinVar release date. The program that performs the update is available on Github.

Credits

Thanks to NCBI for making the ClinVar data available on their FTP site as a tab-separated file.

References

Landrum MJ, Lee JM, Benson M, Brown G, Chao C, Chitipiralla S, Gu B, Hart J, Hoffman D, Hoover J et al. ClinVar: public archive of interpretations of clinically relevant variants. Nucleic Acids Res. 2016 Jan 4;44(D1):D862-8. PMID: 26582918; PMC: PMC4702865