Schema for ClinVar Lift - Human ClinVar variants lifted to Rhesus
  Database: rheMac10    Primary Table: clinvarLift Data last updated: 2020-03-04
Big Bed File Download: /gbdb/rheMac10/bbi/
Item Count: 610,464
The data is stored in the binary BigBed format.

Format description: Browser extensible data (12 fields) plus information about a ClinVar entry
chromchr1Chromosome (or contig, scaffold, etc.)
chromStart149260510Start position in chromosome
chromEnd149260511End position in chromosome
nameG>TName of item
score1Score from 0-1000
strand.+ or -
thickStart149260510Start of where display should be thick (start codon)
thickEnd149260511End of where display should be thick (stop codon)
reserved53760Used as itemRgb as of 2004-11-22
blockCount1Number of blocks
blockSizes1,Comma separated list of block sizes
chromStarts0,Start positions relative to chromStart
newNuclCrheMac10 sequence at lifted position
origPoschr1:75156894-75156895Original human hg38 position
origNuclGHuman genome forward strand sequence
origName782378|NM_001001933.1(LHX8):c.813G>T (p.Val271=)ClinVar Variation Report
clinSignBenignClinical significance
reviewStatus★☆☆☆  based on: criteria provided,single submitterReview Status
typesingle nucleotide variantType of Variant
geneId431707|LHX8Human Gene Symbol
snpIddbSNP ID
nsvIddbVar ID
rcvAccRCV000963759ClinVar Allele Submission
testedInGtrNGenetic Testing Registry
phenotypeListnot providedHuman Phenotypes
phenotypeMedGen:CN517202Phenotype identifiers
origingermlineData origin
assemblyGRCh38Genome assembly
cytogenetic1p31.1Cytogenetic status
hgvsCodNM_001256114.2:c.783G>TNucleotide HGVS
hgvsProtNP_001243043.1:p.Val261=Protein HGVS
numSubmit1Number of submitters
lastEvalAug 17,2018Last evaluation
otherIdsOther identifiers e.g. OMIM IDs, etc.
_mouseOverc.813G>T, Benign, 1 stars, Phenotypes: not provided, Origin: germline, 1 submittersMouse over text
_clinSignCodeBNClinical Significance
_varLen1Variant Length in base pairs

Sample Rows
chr1149260510149260511G>T1.1492605101492605115376011,0,Cchr1:75156894-75156895G782378|NM_001001933.1(LHX8):c.813G>T (p.Val271=)Benign★☆☆☆  based on: criteria provided,single submittersingle nucleotide variant431707|LHX8RCV000963759Nnot providedMedGen:CN517202germlineGRCh381p31.1NM_001256114.2:c.783G>TNP_001243043.1:p.Val261=1Aug 17,2018c.813G>T, Benign, 1 stars, Phenotypes: not provided, Origin: germline, 1 submittersBN1
chr1149273949149273950C>T1.1492739491492739505376011,0,Gchr1:75143168-75143169C787749|NM_001001933.1(LHX8):c.441C>T (p.Asp147=)Benign★☆☆☆  based on: criteria provided,single submittersingle nucleotide variant431707|LHX8RCV000970049Nnot providedMedGen:CN517202germlineGRCh381p31.1NM_001256114.2:c.411C>TNP_001243043.1:p.Asp137=1May 18,2018c.441C>T, Benign, 1 stars, Phenotypes: not provided, Origin: germline, 1 submittersBN1
chr1149279995149279996C>T1.1492799951492799965376011,0,Gchr1:75137115-75137116C787748|NM_001001933.1(LHX8):c.122C>T (p.Ala41Val)Benign★☆☆☆  based on: criteria provided,single submittersingle nucleotide variant431707|LHX8RCV000970048Nnot providedMedGen:CN517202germlineGRCh381p31.1NM_001256114.2:c.92C>TNP_001243043.1:p.Ala31Val1May 18,2018c.122C>T, Benign, 1 stars, Phenotypes: not provided, Origin: germline, 1 submittersBN1
chr1149687127149687128G>A1.1496871271496871285376011,0,Gchr1:74719372-74719373C771689|NM_001889.4(CRYZ):c.265-1G>ALikely benign★☆☆☆  based on: criteria provided,single submittersingle nucleotide variant1429|CRYZRCV000951049Nnot providedMedGen:CN517202germlineGRCh381p31.1NM_001889.4:c.265-1G>A1Jan 04,2019c.265-1G>A, Likely benign, 1 stars, Phenotypes: not provided, Origin: germline, 1 submittersLB1
chr1149696701149696702G>A1.1496967011496967025376011,0,Gchr1:74710180-74710181C783288|NM_001889.4(CRYZ):c.547G>A (p.Glu183Lys)Benign★☆☆☆  based on: criteria provided,single submittersingle nucleotide variant1429|CRYZRCV000964813Nnot providedMedGen:CN517202germlineGRCh381p31.1NM_001889.4:c.547G>ANP_001880.2:p.Glu183Lys1Jul 23,2018c.547G>A, Benign, 1 stars, Phenotypes: not provided, Origin: germline, 1 submittersBN1
chr1149699738149699739G>A1.1496997381496997395376011,0,Gchr1:74707101-74707102C728987|NM_001889.4(CRYZ):c.732+1G>ALikely benign★☆☆☆  based on: criteria provided,single submittersingle nucleotide variant1429|CRYZRCV000903566Nnot providedMedGen:CN517202germlineGRCh381p31.1NM_001889.4:c.732+1G>A1Jul 23,2018c.732+1G>A, Likely benign, 1 stars, Phenotypes: not provided, Origin: germline, 1 submittersLB1
chr1149700467149700468T>C1.1497004671497004685376011,0,Tchr1:74706372-74706373A728063|NM_001889.4(CRYZ):c.913T>C (p.Leu305=)Benign★☆☆☆  based on: criteria provided,single submittersingle nucleotide variant1429|CRYZRCV000902480Nnot providedMedGen:CN517202germlineGRCh381p31.1NM_001889.4:c.913T>CNP_001880.2:p.Leu305=1Dec 11,2018c.913T>C, Benign, 1 stars, Phenotypes: not provided, Origin: germline, 1 submittersBN1
chr1149915120149915121G>A1.1499151201499151211376256011,0,Cchr1:74492216-74492217G626247|NM_015978.3(TNNI3K):c.2302G>A (p.Glu768Lys)Likely pathogenic★☆☆☆  based on: criteria provided,single submittersingle nucleotide variant51086|TNNI3K202238194RCV000768402NCardiac conduction disease with or without dilated cardiomyopathyMedGen:C4015285, ...germline,inheritedGRCh381p31.1NM_015978.3:c.2302G>ANP_057062.1:p.Glu768Lys2Apr 23,2019OMIM Allelic Variant:613932.0004c.2302G>A, Likely pathogenic, 1 stars, Phenotypes: Cardiac conduction disease with or without dilated cardiomyopathy, Origin: ge ...LP1
chr1149918180149918181A>G1.1499181801499181815376011,0,Tchr1:74489215-74489216A740641|NM_015978.3(TNNI3K):c.2149A>G (p.Met717Val)Likely benign★☆☆☆  based on: criteria provided,single submittersingle nucleotide variant51086|TNNI3KRCV000916727Nnot providedMedGen:CN517202germlineGRCh381p31.1NM_015978.3:c.2149A>GNP_057062.1:p.Met717Val1Jul 16,2018c.2149A>G, Likely benign, 1 stars, Phenotypes: not provided, Origin: germline, 1 submittersLB1
chr1149961414149961415C>T1.1499614141499614155376011,0,Gchr1:74439520-74439521C725704|NM_015978.3(TNNI3K):c.1910C>T (p.Thr637Met)Benign★☆☆☆  based on: criteria provided,single submittersingle nucleotide variant51086|TNNI3KRCV000899809Nnot providedMedGen:CN517202germlineGRCh381p31.1NM_015978.3:c.1910C>TNP_057062.1:p.Thr637Met1May 25,2018c.1910C>T, Benign, 1 stars, Phenotypes: not provided, Origin: germline, 1 submittersBN1

ClinVar Lift (clinvarLift) Track Description


This track shows human clinically relevant variants from the ClinVar database, mapped from hg38 to the rheMac10 genome. The mapping uses UCSC's whole-genome alignments and the tool LiftOver. The annotations are somewhat speculative, as LiftOver is not meant to be used for cross-organism mapping. Among others, LiftOver has no notion of phylogenetic trees or protein orthology, so the exact protein to which they are mapped may not be the annotated ortholog. In areas with protein repeats it may have been mapped to the wrong exon. When the genome nucleotide in rheMac10 is different from hg38, the corresponding position could be several basepairs away. Generally, the more different the gene, the harder the mapping. Before planning assays on these data, a manual alignment and annotation of the human and rheMac10 nucleotide or amino acid sequences is recommended.

Display Conventions and Configuration

Genomic locations of ClinVar variants are labeled with the human ClinVar variant descriptions. For example, the label "C>G" usually means that in human, the cDNA nucleotide change is from C>T. On a transcript on the reverse strand, the human genome nucleotide on the forward strand would be G. In rheMac10, the genome may not be G at this position. Zoom in to see the nucleotide in rheMac10, or click the variant to show the human position and nucleotide and the rheMac10 nucleotide.

All ClinVar information related to each is variant is shown on that variant's details page. Hold the mouse over a feature to show the clinical significance of a variant in humans.

Only short variants with a length < 10 bp on the human genome were lifted. A few variants that after lifting result in rheMac10 annotations longer than 30bp were filtered out, too. This can happen in repetitive regions that are hard to align.

Annotations 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 is updated every month, but these mappings are not updated yet on a regular schedule. Please contact us if you are interested in regular updates.

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 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 -chrom=chr1 -start=0 -end=100000000 stdout


The hg38 ClinvarMain track was annotated with nucleotides and positions, lifted to rheMac10, filtered again for variants < 30bp and annotated with nucleotides again. The output was converted to the bigBed format. The program that performs the mapping is available on Github.


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


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