Schema for ClinVar Variants - ClinVar Variants
  Database: hg38    Primary Table: clinvarCnv Data last updated: 2024-01-24
Big Bed File Download: /gbdb/hg38/bbi/clinvar/clinvarCnv.bb
Item Count: 21,513
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
namenssv3397176Name 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)
reserved0,0,179Used as itemRgb as of 2004-11-22
blockCount1Number of blocks
blockSizes30412929Comma separated list of block sizes
chromStarts0Start positions relative to chromStart
origName155448|VCV000155448 : GRCh38/hg38 1q21.2-25.2(chr1:149854269-180267197)x3Link to ClinVar with Variant ID
clinSignPathogenicClinical significance
reviewStatus☆☆☆☆  based on: no assertion criteria providedReview Status
typecopy number gainType of Variant
geneIdsubset of 1587 genes: ASH1L:FLG:GATAD2B:LHX4:LMNA:PBX1:POGZ:SDHC:SF3B4Gene Symbol
molConseqMolecular Consequence
snpIdrs-1dbSNP ID
nsvIdnsv995575dbVar ID
rcvAccRCV000143515ClinVar Allele Submission
testedInGtrNGenetic Testing Registry
phenotypeListSee casesPhenotypes
phenotypePhenotype identifiers
originnot providedAllele origin
assemblyGRCh38Genome assembly
cytogenetic1q21.2-25.2Cytogenetic status
_jsonHgvsTable[["g.(?_149854269)_(180267197_?)dup", "-"]]HGVS names
_hgvsProtProtein HGVS
numSubmit1Number of submitters
lastEvalJul 16,2013Last evaluation
guidelinesACMG2013,ACMG2016,ACMG2021,ACMG2022Guidelines
otherIdsdbVar:nssv3397176Other identifiers (ClinGen, OMIM, etc.)
_mouseOverGRCh38/hg38 1q21.2-25.2(chr1:149854269-180267197)x3
Review Status: ☆☆☆☆  based on: no assertion criteria provided
Type: copy number gain
Consequence:
Significance: Pathogenic
Origin: not provided
Phenotypes: See cases
Mouse over text
_clinSignCodePGClinical Significance
_originCodeUNKAllele Origin Code
_allTypeCodeGAINVariation Type
_varLen30412929Variant Length in base pairs
_starCount0Number of stars
_variantId155448ClinVar variant ID
_dbVarSsvIdnssv3397176dbVar SSV ID

Sample Rows
 
chromchromStartchromEndnamescorestrandthickStartthickEndreservedblockCountblockSizeschromStartsorigNameclinSignreviewStatustypegeneIdmolConseqsnpIdnsvIdrcvAcctestedInGtrphenotypeListphenotypeoriginassemblycytogenetic_jsonHgvsTable_hgvsProtnumSubmitlastEvalguidelinesotherIds_mouseOver_clinSignCode_originCode_allTypeCode_varLen_starCount_variantId_dbVarSsvId
chr1149854268180267197nssv33971760.1498542681802671970,0,1791304129290155448|VCV000155448 : GRCh38/hg38 1q21.2-25.2(chr1:149854269-180267197)x3Pathogenic☆☆☆☆  based on: no assertion criteria providedcopy number gainsubset of 1587 genes: ASH1L:FLG:GATAD2B:LHX4:LMNA:PBX1:POGZ:SDHC:SF3B4rs-1nsv995575RCV000143515NSee casesnot providedGRCh381q21.2-25.2[["g.(?_149854269)_(180267197_?)dup", "-"]]1Jul 16,2013ACMG2013,ACMG2016,ACMG2021,ACMG2022dbVar:nssv3397176GRCh38/hg38 1q21.2-25.2(chr1:149854269-180267197)x3Review Status: ☆☆☆☆  base ...PGUNKGAIN304129290155448nssv3397176
chr1157747245176021247nssv5785351.1577472451760212470,0,179118274002058109|VCV000058109 : GRCh38/hg38 1q23.1-25.1(chr1:157747246-176021247)x3Pathogenic★☆☆☆  based on: criteria provided,single submittercopy number gainsubset of 777 genes: PBX1:SDHCrs-1nsv530567RCV000051854NSee casesnot providedGRCh381q23.1-25.1[["g.(?_157747246)_(176021247_?)dup", "-"]]1Aug 12,2011ACMG2013,ACMG2016,ACMG2021,ACMG2022dbVar:nssv578535GRCh38/hg38 1q23.1-25.1(chr1:157747246-176021247)x3Review Status: ★☆☆☆  base ...PGUNKGAIN18274002158109nssv578535
chr1159479886166895086nssv5772271.159479886166895086153,0,017415200057465|VCV000057465 : GRCh38/hg38 1q23.2-24.1(chr1:159479887-166895086)x1Pathogenic★☆☆☆  based on: criteria provided,single submittercopy number losssubset of 373 genes: PBX1:SDHCrs-1nsv529716RCV000051172NSee casesnot providedGRCh381q23.2-24.1[["g.(?_159479887)_(166895086_?)del", "-"]]1Aug 12,2011ACMG2013,ACMG2016,ACMG2021,ACMG2022dbVar:nssv577227GRCh38/hg38 1q23.2-24.1(chr1:159479887-166895086)x1Review Status: ★☆☆☆  base ...PGUNKLOSS7415200157465nssv577227
chr1161740906173965154nssv5772291.161740906173965154153,0,0112224248060042|VCV000060042 : GRCh38/hg38 1q23.3-25.1(chr1:161740907-173965154)x1Pathogenic★☆☆☆  based on: criteria provided,single submittercopy number losssubset of 408 genes: PBX1rs-1nsv532581RCV000053914NSee casesde novoGRCh381q23.3-25.1[["g.(?_161740907)_(173965154_?)del", "-"]]1Aug 12,2011dbVar:nssv577229GRCh38/hg38 1q23.3-25.1(chr1:161740907-173965154)x1Review Status: ★☆☆☆  base ...PGGERMLOSS12224248160042nssv577229
chr1162040049167480663nssv5772301.162040049167480663153,0,015440614060043|VCV000060043 : GRCh38/hg38 1q23.3-24.2(chr1:162040050-167480663)x1Pathogenic★☆☆☆  based on: criteria provided,single submittercopy number losssubset of 153 genes: PBX1rs-1nsv532582RCV000053915NSee casesnot providedGRCh381q23.3-24.2[["g.(?_162040050)_(167480663_?)del", "-"]]1Aug 12,2011dbVar:nssv577230GRCh38/hg38 1q23.3-24.2(chr1:162040050-167480663)x1Review Status: ★☆☆☆  base ...PGUNKLOSS5440614160043nssv577230
chr1163382522175877022nssv16104540.163382522175877022153,0,01124945000155225|VCV000155225 : GRCh38/hg38 1q23.3-25.1(chr1:163382523-175877022)x1Pathogenic☆☆☆☆  based on: no assertion criteria providedcopy number losssubset of 409 genes: PBX1rs-1nsv932260RCV000143292NSee casesnot providedGRCh381q23.3-25.1[["g.(?_163382523)_(175877022_?)del", "-"]]1Mar 19,2013dbVar:nssv1610454GRCh38/hg38 1q23.3-25.1(chr1:163382523-175877022)x1Review Status: ☆☆☆☆  base ...PGUNKLOSS124945000155225nssv1610454
chr1164922654180061589nssv5785371.1649226541800615890,0,179115138935058111|VCV000058111 : GRCh38/hg38 1q23.3-25.2(chr1:164922655-180061589)x3Pathogenic★☆☆☆  based on: criteria provided,single submittercopy number gaincovers 484 genes,none of which curated to show dosage sensitivityrs-1nsv530569RCV000051856NSee casesnot providedGRCh381q23.3-25.2[["g.(?_164922655)_(180061589_?)dup", "-"]]1Aug 12,2011dbVar:nssv578537GRCh38/hg38 1q23.3-25.2(chr1:164922655-180061589)x3Review Status: ★☆☆☆  base ...PGUNKGAIN15138935158111nssv578537
chr1166031545166979276nssv16027260.166031545166979276255,0,019477310150235|VCV000150235 : GRCh38/hg38 1q24.1(chr1:166031546-166979276)x1Uncertain significance☆☆☆☆  based on: no assertion criteria providedcopy number losscovers 35 genes,none of which curated to show dosage sensitivityrs-1nsv916491RCV000139120NSee casesnot providedGRCh381q24.1[["g.(?_166031546)_(166979276_?)del", "-"]]1Jul 09,2012dbVar:nssv1602726GRCh38/hg38 1q24.1(chr1:166031546-166979276)x1Review Status: ☆☆☆☆  based on: ...VUSUNKLOSS9477310150235nssv1602726
chr1166762831175327423nssv5772321.166762831175327423153,0,018564592060045|VCV000060045 : GRCh38/hg38 1q24.1-25.1(chr1:166762832-175327423)x1Pathogenic★☆☆☆  based on: criteria provided,single submittercopy number losscovers 334 genes,none of which curated to show dosage sensitivityrs-1nsv532584RCV000053917NSee casesde novoGRCh381q24.1-25.1[["g.(?_166762832)_(175327423_?)del", "-"]]1Aug 12,2011dbVar:nssv577232GRCh38/hg38 1q24.1-25.1(chr1:166762832-175327423)x1Review Status: ★☆☆☆  base ...PGGERMLOSS8564592160045nssv577232
chr1167801065167863028nssv16092320.167801065167863028255,98,1191619630151438|VCV000151438 : GRCh38/hg38 1q24.2(chr1:167801066-167863028)x1Likely benign☆☆☆☆  based on: no assertion criteria providedcopy number lossADCY10,LOC129931873rs-1nsv931324RCV000140151NSee casesnot providedGRCh381q24.2[["g.(?_167801066)_(167863028_?)del", "-"]]1Apr 30,2011dbVar:nssv1609232GRCh38/hg38 1q24.2(chr1:167801066-167863028)x1Review Status: ☆☆☆☆  based on: ...LBUNKLOSS619630151438nssv1609232

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.

These tracks show 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 ClinVar SNVs track displays substitutions and indels shorter than 50 bp and the ClinVar CNVs track displays copy number variants (CNVs) equal or larger than 50 bp. Until October 2017, all variants with the ClinVar types copy number gain/loss and DbVar "nsv" accessions were assigned in the CNV category. Because the ClinVar type no longer captures this information, any variation equal to or larger than 50 bp is now considered a CNV.

The ClinVar Interpretations track displays the genomic positions of individual variant submissions and interpretations of the clinical significance and their relationship to disease in the ClinVar database.

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

Items can be filtered according to the size of the variant, variant type, clinical significance, allele origin, and molecular consequence, using the track Configure options. Each subtrack has separate display controls, as described here.

Mouseover on the genomic locations of ClinVar variants shows variant details, clinical interpretation, and associated conditions. Further information on each variant is displayed on the details page by a click onto any variant. ClinVar is an archive for assertions of clinical significance made by the submitters. The level of review supporting the assertion of clinical significance for the variation is reported as the review status. Stars (0 to 4) provide a graphical representation of the aggregate review status.

Entries in the ClinVar CNVs track are colored by type of variant, among others:

  • red for loss
  • blue for gain
  • purple for inversion
  • orange for insertion
A light-to-dark color gradient indicates the clinical significance of each variant, with the lightest shade being benign, to the darkest shade being pathogenic. Detailed information on the CNV color code is described here.

Entries in the ClinVar SNVs and ClinVar Interpretations tracks are colored by clinical significance:

  • red for pathogenic
  • dark blue for variant of uncertain significance
  • green for benign
  • dark grey for not provided
  • light blue for conflicting

The variants in the ClinVar Interpretations track are sorted by the variant classification of each submission:

  • P: Pathogenic
  • LP: Likely Pathogenic
  • VUS: Variant of Unknown Significance
  • LB: Likely Benign
  • B: Benign
  • OTH: Others
The size of the bead represents the number of submissions at that genomic position. For track display clarity, these submission numbers are binned into three categories:
  • Small-sized beads: 1-2 submissions
  • Medium-sized beads: 3-7 submissions
  • Large-sized beads: 8 or more submissions
Hovering on the track items shows the genomic variations which start at that position and the number of individual submissions with that classification. The details page lists all rated submissions from ClinVar, with specific details to the interpretation of the clinical or functional significance of each variant in relation to a condition. Interpretation is at variant-level, not at case (or patient-specific) level.

More information about using and understanding the ClinVar data can be found here.

For the human genome version hg19: the hg19 genome released by UCSC in 2009 had a mitochondrial genome "chrM" that was not the same as the one later used for most databases like ClinVar. As a result, we added the official mitochondrial genome in 2020 as "chrMT" and all mitochondrial annotations of ClinVar and most other databases are shown on the mitochondrial genome called "chrMT". For full description of the issue of the mitochondrial genome in hg19, please see the README file on our download site.

Data updates

ClinVar publishes a new release on the first Thursday every month. This track is then 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 display one of these previous versions, paste the URL to one of the older files into the custom track text input field under "My Data > Custom Tracks".

Data access

The raw data can be explored interactively with the Table Browser or the Data Integrator. The data can be accessed from scripts through our API, the track names are "clinVarMain and "clinVarCnv".

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

Azzariti DR, Riggs ER, Niehaus A, Rodriguez LL, Ramos EM, Kattman B, Landrum MJ, Martin CL, Rehm HL. Points to consider for sharing variant-level information from clinical genetic testing with ClinVar. Cold Spring Harb Mol Case Stud. 2018 Feb;4(1). PMID: 29437798; PMC: PMC5793773