Schema for ClinVar Variants - ClinVar Variants
  Database: hg38    Primary Table: clinvarMain Data last updated: 2024-01-24
Big Bed File Download: /gbdb/hg38/bbi/clinvar/clinvarMain.bb
Item Count: 2,347,028
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.)
chromStart166070274Start position in chromosome
chromEnd166070275End position in chromosome
nameG>AName of item
score1Score from 0-1000
strand.+ or -
thickStart166070274Start of where display should be thick (start codon)
thickEnd166070275End of where display should be thick (stop codon)
reserved0,0,128Used as itemRgb as of 2004-11-22
blockCount1Number of blocks
blockSizes1Comma separated list of block sizes
chromStarts0Start positions relative to chromStart
origName2344018|VCV002344018 : NM_001017961.5(FAM78B):c.752G>A (p.Arg251Gln)Link to ClinVar with Variant ID
clinSignUncertain significanceClinical significance
reviewStatus★☆☆☆  based on: criteria provided,single submitterReview Status
typesingle nucleotide variantType of Variant
geneId149297|FAM78BGene Symbol
molConseqmissense variantMolecular Consequence
snpIdrs-1dbSNP ID
nsvIddbVar ID
rcvAccRCV002931351ClinVar Allele Submission
testedInGtrNGenetic Testing Registry
phenotypeListInborn genetic diseasesPhenotypes
phenotypeMeSH:D030342, MedGen:C0950123Phenotype identifiers
origingermlineAllele origin
assemblyGRCh38Genome assembly
cytogenetic1q24.1Cytogenetic status
_jsonHgvsTable[["c.752G>A", "-"], ["g.166070275C>T", "-"], ["c.752G>A", "p.Arg251Gln"], ["n.1505G>A", "-"], ["n.1259G>A", "-"], ["c.264-9612G>A", "-"]]HGVS names
_hgvsProtProtein HGVS
numSubmit1Number of submitters
lastEvalOct 12,2021Last evaluation
guidelinesGuidelines
otherIdsOther identifiers (ClinGen, OMIM, etc.)
_mouseOverNM_001017961.5(FAM78B):c.752G>A (p.Arg251Gln)
Review Status: ★☆☆☆  based on: criteria provided,single submitter
Type: single nucleotide variant
Consequence: missense variant
Significance: Uncertain significance
Origin: germline
Phenotypes: Inborn genetic diseases
Mouse over text
_clinSignCodeVUSClinical Significance
_originCodeGERMAllele Origin Code
_allTypeCodeSUBSTVariation Type
_varLen1Variant Length in base pairs
_starCount1Number of stars
_variantId2344018ClinVar variant ID
_dbVarSsvIddbVar SSV ID

Sample Rows
 
chromchromStartchromEndnamescorestrandthickStartthickEndreservedblockCountblockSizeschromStartsorigNameclinSignreviewStatustypegeneIdmolConseqsnpIdnsvIdrcvAcctestedInGtrphenotypeListphenotypeoriginassemblycytogenetic_jsonHgvsTable_hgvsProtnumSubmitlastEvalguidelinesotherIds_mouseOver_clinSignCode_originCode_allTypeCode_varLen_starCount_variantId_dbVarSsvId
chr1166070274166070275G>A1.1660702741660702750,0,1281102344018|VCV002344018 : NM_001017961.5(FAM78B):c.752G>A (p.Arg251Gln)Uncertain significance★☆☆☆  based on: criteria provided,single submittersingle nucleotide variant149297|FAM78Bmissense variantrs-1RCV002931351NInborn genetic diseasesMeSH:D030342, MedGen:C0950123germlineGRCh381q24.1[["c.752G>A", "-"], ["g.166070275C>T", "-"], ["c.752G>A", "p.Arg251Gln"], ["n.1505G>A", "-"], ["n.1259G>A", "-"], ["c.264-9612G> ...1Oct 12,2021NM_001017961.5(FAM78B):c.752G>A (p.Arg251Gln)Review Status: ★☆☆☆  based on: ...VUSGERMSUBST112344018
chr1166070288166070289G>A1.1660702881660702890,0,1281102612468|VCV002612468 : NM_001017961.5(FAM78B):c.738G>A (p.Met246Ile)Uncertain significance★☆☆☆  based on: criteria provided,single submittersingle nucleotide variant149297|FAM78Bmissense variantrs-1RCV003371440NInborn genetic diseasesMeSH:D030342, MedGen:C0950123germlineGRCh381q24.1[["c.738G>A", "-"], ["g.166070289C>T", "-"], ["c.738G>A", "p.Met246Ile"], ["n.1491G>A", "-"], ["n.1245G>A", "-"], ["c.264-9626G> ...1Jul 17,2023NM_001017961.5(FAM78B):c.738G>A (p.Met246Ile)Review Status: ★☆☆☆  based on: ...VUSGERMSUBST112612468
chr1166070352166070353G>A1.1660703521660703530,0,1281102357485|VCV002357485 : NM_001017961.5(FAM78B):c.674G>A (p.Arg225Gln)Uncertain significance★☆☆☆  based on: criteria provided,single submittersingle nucleotide variant149297|FAM78Bmissense variantrs-1RCV002969830NInborn genetic diseasesMeSH:D030342, MedGen:C0950123germlineGRCh381q24.1[["g.166070353C>T", "-"], ["c.674G>A", "p.Arg225Gln"], ["n.1427G>A", "-"], ["n.1181G>A", "-"], ["c.264-9690G>A", "-"], ["c.674G> ...1Dec 06,2022NM_001017961.5(FAM78B):c.674G>A (p.Arg225Gln)Review Status: ★☆☆☆  based on: ...VUSGERMSUBST112357485
chr1166070364166070365G>A1.1660703641660703650,0,1281102347638|VCV002347638 : NM_001017961.5(FAM78B):c.662G>A (p.Arg221Gln)Uncertain significance★☆☆☆  based on: criteria provided,single submittersingle nucleotide variant149297|FAM78Bmissense variantrs-1RCV002963776NInborn genetic diseasesMeSH:D030342, MedGen:C0950123germlineGRCh381q24.1[["g.166070365C>T", "-"], ["c.662G>A", "p.Arg221Gln"], ["n.1415G>A", "-"], ["n.1169G>A", "-"], ["c.264-9702G>A", "-"], ["c.662G> ...1Oct 20,2021NM_001017961.5(FAM78B):c.662G>A (p.Arg221Gln)Review Status: ★☆☆☆  based on: ...VUSGERMSUBST112347638
chr1166070461166070462A>G1.1660704611660704620,0,1281102227178|VCV002227178 : NM_001017961.5(FAM78B):c.565A>G (p.Ile189Val)Uncertain significance★☆☆☆  based on: criteria provided,single submittersingle nucleotide variant149297|FAM78Bmissense variantrs-1RCV002678730NInborn genetic diseasesMeSH:D030342, MedGen:C0950123germlineGRCh381q24.1[["c.565A>G", "-"], ["g.166070462T>C", "-"], ["c.565A>G", "p.Ile189Val"], ["n.1318A>G", "-"], ["n.1072A>G", "-"], ["c.264-9799A> ...1Oct 12,2021NM_001017961.5(FAM78B):c.565A>G (p.Ile189Val)Review Status: ★☆☆☆  based on: ...VUSGERMSUBST112227178
chr1166070490166070491C>T1.1660704901660704910,0,1281102550630|VCV002550630 : NM_001017961.5(FAM78B):c.536C>T (p.Thr179Ile)Uncertain significance★☆☆☆  based on: criteria provided,single submittersingle nucleotide variant149297|FAM78Bmissense variantrs-1RCV003258349NInborn genetic diseasesMeSH:D030342, MedGen:C0950123germlineGRCh381q24.1[["c.536C>T", "-"], ["g.166070491G>A", "-"], ["c.536C>T", "p.Thr179Ile"], ["n.1289C>T", "-"], ["n.1043C>T", "-"], ["c.264-9828C> ...1May 23,2023NM_001017961.5(FAM78B):c.536C>T (p.Thr179Ile)Review Status: ★☆☆☆  based on: ...VUSGERMSUBST112550630
chr1166070652166070653T>C1.1660706521660706530,0,1281102225268|VCV002225268 : NM_001017961.5(FAM78B):c.374T>C (p.Val125Ala)Uncertain significance★☆☆☆  based on: criteria provided,single submittersingle nucleotide variant149297|FAM78Bmissense variantrs-1RCV002722534NInborn genetic diseasesMeSH:D030342, MedGen:C0950123germlineGRCh381q24.1[["c.374T>C", "-"], ["g.166070653A>G", "-"], ["c.374T>C", "p.Val125Ala"], ["n.1127T>C", "-"], ["n.881T>C", "-"], ["c.264-9990T>C ...1Jul 28,2021NM_001017961.5(FAM78B):c.374T>C (p.Val125Ala)Review Status: ★☆☆☆  based on: ...VUSGERMSUBST112225268
chr1166840968166840969G>T1.1668409681668409690,0,1281102330741|VCV002330741 : NM_017542.5(POGK):c.13G>T (p.Ala5Ser)Uncertain significance★☆☆☆  based on: criteria provided,single submittersingle nucleotide variant57645|POGKmissense variantrs-1RCV002935092NInborn genetic diseasesMeSH:D030342, MedGen:C0950123germlineGRCh381q24.1[["c.13G>T", "-"], ["g.166840969G>T", "-"], ["c.-116G>T", "-"], ["c.13G>T", "p.Ala5Ser"]]1Dec 01,2022NM_017542.5(POGK):c.13G>T (p.Ala5Ser)Review Status: ★☆☆☆  based on: criteria ...VUSGERMSUBST112330741
chr1166840978166840979T>G1.1668409781668409790,0,1281102492644|VCV002492644 : NM_017542.5(POGK):c.23T>G (p.Leu8Arg)Uncertain significance★☆☆☆  based on: criteria provided,single submittersingle nucleotide variant57645|POGKmissense variantrs-1RCV003218005NInborn genetic diseasesMeSH:D030342, MedGen:C0950123germlineGRCh381q24.1[["c.23T>G", "-"], ["g.166840979T>G", "-"], ["c.-106T>G", "-"], ["c.23T>G", "p.Leu8Arg"]]1Mar 01,2023NM_017542.5(POGK):c.23T>G (p.Leu8Arg)Review Status: ★☆☆☆  based on: criteria ...VUSGERMSUBST112492644
chr1166846647166846648T>A1.1668466471668466480,0,1281102554349|VCV002554349 : NM_017542.5(POGK):c.169T>A (p.Ser57Thr)Uncertain significance★☆☆☆  based on: criteria provided,single submittersingle nucleotide variant57645|POGKmissense variantrs-1RCV003304278NInborn genetic diseasesMeSH:D030342, MedGen:C0950123germlineGRCh381q24.1[["c.169T>A", "-"], ["g.166846648T>A", "-"], ["c.169T>A", "p.Ser57Thr"], ["c.5-2290T>A", "-"]]1May 31,2023NM_017542.5(POGK):c.169T>A (p.Ser57Thr)Review Status: ★☆☆☆  based on: criter ...VUSGERMSUBST112554349

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