Schema for ClinVar Variants - ClinVar Variants
  Database: hg38    Primary Table: clinvarMain Data last updated: 2020-06-17
Big Bed File: /gbdb/hg38/bbi/clinvar/clinvarMain.bb
Item Count: 718,575
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.)
chromStart166849448Start position in chromosome
chromEnd166849449End position in chromosome
nameC>TName of item
score1Score from 0-1000
strand.+ or -
thickStart166849448Start of where display should be thick (start codon)
thickEnd166849449End of where display should be thick (stop codon)
reserved0,210,0Used as itemRgb as of 2004-11-22
blockCount1Number of blocks
blockSizes1Comma separated list of block sizes
chromStarts0Start positions relative to chromStart
origName783953|NM_017542.5(POGK):c.870C>T (p.Leu290=)Link to ClinVar
clinSignBenignClinical significance
reviewStatus★☆☆☆  based on: criteria provided,single submitterReview Status
typesingle nucleotide variantType of Variant
geneId57645|POGKGene Symbol
molConseqsynonymous variantMolecular Consequence
snpIddbSNP ID
nsvIddbVar ID
rcvAccRCV000965572ClinVar Allele Submission
testedInGtrNGenetic Testing Registry
phenotypeListnot providedPhenotypes
phenotypeMedGen:CN517202Phenotype identifiers
origingermlineAllele origin
assemblyGRCh38Genome assembly
cytogenetic1q24.1Cytogenetic status
hgvsCodNM_017542.4:c.870C>TNucleotide HGVS
hgvsProtProtein HGVS
numSubmit1Number of submitters
lastEvalApr 24,2018Last evaluation
guidelinesGuidelines
otherIdsOther identifiers e.g. OMIM IDs, etc.
_mouseOverNM_017542.5(POGK):c.870C>T (p.Leu290=), Type: single nucleotide variant, Consequence: synonymous variant, Significance: Benign, Origin: germline, Phenotypes: not providedMouse over text
_clinSignCodeBNClinical Significance
_originCodeGERMAllele Origin Code
_allTypeCodeSNVVariation Type
_varLen1Variant Length in base pairs
_starCount1 number of stars

Sample Rows
 
chromchromStartchromEndnamescorestrandthickStartthickEndreservedblockCountblockSizeschromStartsorigNameclinSignreviewStatustypegeneIdmolConseqsnpIdnsvIdrcvAcctestedInGtrphenotypeListphenotypeoriginassemblycytogenetichgvsCodhgvsProtnumSubmitlastEvalguidelinesotherIds_mouseOver_clinSignCode_originCode_allTypeCode_varLen_starCount
chr1166849448166849449C>T1.1668494481668494490,210,0110783953|NM_017542.5(POGK):c.870C>T (p.Leu290=)Benign★☆☆☆  based on: criteria provided,single submittersingle nucleotide variant57645|POGKsynonymous variantRCV000965572Nnot providedMedGen:CN517202germlineGRCh381q24.1NM_017542.4:c.870C>T1Apr 24,2018NM_017542.5(POGK):c.870C>T (p.Leu290=), Type: single nucleotide variant, Consequence: synonymous variant, Significance: Benign, ...BNGERMSNV11
chr1166863910166863911A>T1.1668639101668639110,210,0110715435|NM_053053.4(TADA1):c.243A>T (p.Gly81=)Benign★☆☆☆  based on: criteria provided,single submittersingle nucleotide variant117143|TADA1synonymous variantRCV000887912Nnot providedMedGen:CN517202germlineGRCh381q24.1NM_053053.3:c.243A>T1Oct 17,2017NM_053053.4(TADA1):c.243A>T (p.Gly81=), Type: single nucleotide variant, Consequence: synonymous variant, Significance: Benign, ...BNGERMSNV11
chr1166957928166957929C>T1.1669579281669579290,210,0110724722|NM_199351.3(ILDR2):c.219C>T (p.Ser73=)Benign★☆☆☆  based on: criteria provided,single submittersingle nucleotide variant387597|ILDR2synonymous variantRCV000898684Nnot providedMedGen:CN517202germlineGRCh381q24.1NM_199351.2:c.219C>T1Apr 24,2018NM_199351.3(ILDR2):c.219C>T (p.Ser73=), Type: single nucleotide variant, Consequence: synonymous variant, Significance: Benign, ...BNGERMSNV11
chr1166992757166992758G>A1.1669927571669927580,210,0110777103|NM_032858.3(MAEL):c.398G>A (p.Arg133His)Benign★☆☆☆  based on: criteria provided,single submittersingle nucleotide variant84944|MAELmissense variantRCV000957520Nnot providedMedGen:CN517202germlineGRCh381q24.1NM_001286378.1:c.230G>ANP_001273307.1:p.Arg77His1Apr 12,2018NM_032858.3(MAEL):c.398G>A (p.Arg133His), Type: single nucleotide variant, Consequence: missense variant, Significance: Benign, ...BNGERMSNV11
chr1167004290167004291C>A1.1670042901670042910,210,0110780787|NM_032858.3(MAEL):c.635C>A (p.Pro212His)Benign★☆☆☆  based on: criteria provided,single submittersingle nucleotide variant84944|MAELmissense variantRCV000961909Nnot providedMedGen:CN517202germlineGRCh381q24.1NM_032858.3:c.635C>ANP_116247.1:p.Pro212His1Dec 31,2019NM_032858.3(MAEL):c.635C>A (p.Pro212His), Type: single nucleotide variant, Consequence: missense variant, Significance: Benign, ...BNGERMSNV11
chr1167055096167055097G>A1.1670550961670550970,210,0110727135|NM_005814.3(GPA33):c.706G>A (p.Ala236Thr)Likely benign★☆☆☆  based on: criteria provided,single submittersingle nucleotide variant10223|GPA33missense variantRCV000901438Nnot providedMedGen:CN517202germlineGRCh381q24.1NM_005814.3:c.706G>ANP_005805.1:p.Ala236Thr1May 10,2018NM_005814.3(GPA33):c.706G>A (p.Ala236Thr), Type: single nucleotide variant, Consequence: missense variant, Significance: Likely ...LBGERMSNV11
chr1167063657167063658G>T1.1670636571670636580,210,0110772820|NM_005814.3(GPA33):c.495G>T (p.Lys165Asn)Benign★☆☆☆  based on: criteria provided,single submittersingle nucleotide variant10223|GPA33missense variantRCV000952461Nnot providedMedGen:CN517202germlineGRCh381q24.1NM_005814.3:c.495G>TNP_005805.1:p.Lys165Asn1Apr 24,2018NM_005814.3(GPA33):c.495G>T (p.Lys165Asn), Type: single nucleotide variant, Consequence: missense variant, Significance: Benign, ...BNGERMSNV11
chr1167068942167068943C>T1.1670689421670689430,210,0110739915|NM_005814.3(GPA33):c.394C>T (p.Arg132Cys)Likely benign★☆☆☆  based on: criteria provided,single submittersingle nucleotide variant10223|GPA33missense variantRCV000915936Nnot providedMedGen:CN517202germlineGRCh381q24.1NM_005814.3:c.394C>TNP_005805.1:p.Arg132Cys1May 10,2018NM_005814.3(GPA33):c.394C>T (p.Arg132Cys), Type: single nucleotide variant, Consequence: missense variant, Significance: Likely ...LBGERMSNV11
chr1167117352167117353A>T1.1671173521671173530,210,0110715851|NM_001080426.3(STYXL2):c.231A>T (p.Ala77=)Benign★☆☆☆  based on: criteria provided,single submittersingle nucleotide variant92235|STYXL2synonymous variantRCV000888388Nnot providedMedGen:CN517202germlineGRCh381q24.1NM_001080426.1:c.231A>T1Apr 30,2018NM_001080426.3(STYXL2):c.231A>T (p.Ala77=), Type: single nucleotide variant, Consequence: synonymous variant, Significance: Beni ...BNGERMSNV11
chr1167119238167119239C>T1.1671192381671192390,210,0110775621|NM_001080426.3(STYXL2):c.438-10C>TBenign★☆☆☆  based on: criteria provided,single submittersingle nucleotide variant92235|STYXL2RCV000955807Nnot providedMedGen:CN517202germlineGRCh381q24.1NM_001080426.3:c.438-10C>T1Apr 10,2018NM_001080426.3(STYXL2):c.438-10C>T, Type: single nucleotide variant, Consequence: , Significance: Benign, Origin: germline, Phen ...BNGERMSNV11

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