Schema for ClinVar Lift - Human ClinVar variants lifted to Mouse
  Database: mm10    Primary Table: clinvarLift Data last updated: 2020-01-31
Big Bed File: /gbdb/mm10/bbi/clinvarLift.bb
Item Count: 575,023
Format description: Browser extensible data (12 fields) plus information about a ClinVar entry
fieldexampledescription
chromchr1Chromosome (or contig, scaffold, etc.)
chromStart130447649Start position in chromosome
chromEnd130447650End position in chromosome
nameG>AName of item
score1Score from 0-1000
strand.+ or -
thickStart130447649Start of where display should be thick (start codon)
thickEnd130447650End 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
newNuclAmm10 sequence at lifted position
origPoschr1:207339388-207339389Original human hg38 position
origNuclGHuman genome forward strand sequence
origName786995|NM_000574.5(CD55):c.1061-8G>AClinVar Variation Report
clinSignBenignClinical significance
reviewStatus★☆☆☆  based on: criteria provided,single submitterReview Status
typesingle nucleotide variantType of Variant
geneId1604|CD55Human Gene Symbol
snpIddbSNP ID
nsvIddbVar ID
rcvAccRCV000969147ClinVar Allele Submission
testedInGtrNGenetic Testing Registry
phenotypeListnot providedHuman Phenotypes
phenotypeMedGen:CN517202Phenotype identifiers
origingermlineData origin
assemblyGRCh38Genome assembly
cytogenetic1q32.2Cytogenetic status
hgvsCodNM_001300902.2:c.1061-8G>ANucleotide HGVS
hgvsProtProtein HGVS
numSubmit1Number of submitters
lastEvalFeb 06,2019Last evaluation
guidelinesGuidelines
otherIdsOther identifiers e.g. OMIM IDs, etc.
_mouseOverc.1061-8G>A, Benign, 1 stars, Phenotypes: not provided, Origin: germline, 1 submittersMouse over text
_clinSignCodeBNClinical Significance
_varLen1Variant Length in base pairs

Sample Rows
 
chromchromStartchromEndnamescorestrandthickStartthickEndreservedblockCountblockSizeschromStartsnewNuclorigPosorigNuclorigNameclinSignreviewStatustypegeneIdsnpIdnsvIdrcvAcctestedInGtrphenotypeListphenotypeoriginassemblycytogenetichgvsCodhgvsProtnumSubmitlastEvalguidelinesotherIds_mouseOver_clinSignCode_varLen
chr1130447649130447650G>A1.1304476491304476505376011,0,Achr1:207339388-207339389G786995|NM_000574.5(CD55):c.1061-8G>ABenign★☆☆☆  based on: criteria provided,single submittersingle nucleotide variant1604|CD55RCV000969147Nnot providedMedGen:CN517202germlineGRCh381q32.2NM_001300902.2:c.1061-8G>A1Feb 06,2019c.1061-8G>A, Benign, 1 stars, Phenotypes: not provided, Origin: germline, 1 submittersBN1
chr1130448345130448346A>G1.1304483451304483465376011,0,Tchr1:207337387-207337388A726239|NM_000574.5(CD55):c.1039A>G (p.Lys347Glu)Benign★☆☆☆  based on: criteria provided,single submittersingle nucleotide variant1604|CD55RCV000900423Nnot providedMedGen:CN517202germlineGRCh381q32.2NR_125349.2:n.1127A>G1Jan 08,2019c.1039A>G, Benign, 1 stars, Phenotypes: not provided, Origin: germline, 1 submittersBN1
chr1130448403130448404A>G1.1304484031304484045376011,0,Gchr1:207337332-207337333A799515|NM_000574.5(CD55):c.984A>G (p.Thr328=)Likely benign★☆☆☆  based on: criteria provided,single submittersingle nucleotide variant1604|CD55RCV000983118Nnot providedMedGen:CN517202germlineGRCh381q32.2NR_125349.2:n.1072A>G1Dec 27,2018c.984A>G, Likely benign, 1 stars, Phenotypes: not provided, Origin: germline, 1 submittersLB1
chr1130452439130452440G>C0.1304524391304524401376256011,0,Cchr1:207331242-207331243G431762|NM_000574.5(CD55):c.800G>C (p.Cys267Ser)Pathogenic☆☆☆☆  based on: no assertion criteria providedsingle nucleotide variant1604|CD551135402917RCV000497257NProtein-losing enteropathyHuman Phenotype Ontology:HP:0002243, MedGen:C4538570, ...germlineGRCh381q32.2NM_001300904.2:c.800G>CNP_001287833.1:p.Cys267Ser1Aug 11,2017OMIM Allelic Variant:125240.0006c.800G>C, Pathogenic, 0 stars, Phenotypes: Protein-losing enteropathy, Origin: germline, 1 submittersPG1
chr1130456888130456889C>T0.1304568881304568891376256011,0,Achr1:207326768-207326769C431759|NM_000574.5(CD55):c.596C>T (p.Ser199Leu)Pathogenic☆☆☆☆  based on: no assertion criteria providedsingle nucleotide variant1604|CD551135402914RCV000497258NCROMER BLOOD GROUP SYSTEM,Dr(a-) PHENOTYPEnagermlineGRCh381q32.2NM_001300904.2:c.596C>TNP_001287833.1:p.Ser199Leu1Sep 01,2017OMIM Allelic Variant:125240.0003, dbRBC - Blood Group Antigen ...c.596C>T, Pathogenic, 0 stars, Phenotypes: CROMER BLOOD GROUP SYSTEM,Dr(a-) PHENOTYPE, Origin: germline, 1 submittersPG1
chr1130459773130459774G>A0.1304597731304597741376256011,0,Cchr1:207324557-207324558G431763|NM_000574.5(CD55):c.287-1G>APathogenic☆☆☆☆  based on: no assertion criteria providedsingle nucleotide variant1604|CD551135402918RCV000497260NProtein-losing enteropathyHuman Phenotype Ontology:HP:0002243, MedGen:C4538570, ...germlineGRCh381q32.2NM_001300902.2:c.287-1G>A1Aug 11,2017OMIM Allelic Variant:125240.0007c.287-1G>A, Pathogenic, 0 stars, Phenotypes: Protein-losing enteropathy, Origin: germline, 1 submittersPG1
chr1130461844130461845C>A0.130461844130461845842150411,0,Gchr1:207322543-207322544C16872|NM_000574.5(CD55):c.263C>A (p.Ser88Ter)Affects☆☆☆☆  based on: no assertion criteria providedsingle nucleotide variant1604|CD551131690771RCV000018368NCromer blood group systemMedGen:C1292305, ...germlineGRCh381q32.2NM_001300904.2:c.263C>ANP_001287833.1:p.Ser88Ter1Jan 15,1998OMIM Allelic Variant:125240.0002c.263C>A, Affects, 0 stars, Phenotypes: Cromer blood group system, Origin: germline, 1 submittersOT1
chr1130461846130461847G>A0.130461846130461847842150411,0,Cchr1:207322541-207322542G16871|NM_000574.5(CD55):c.261G>A (p.Trp87Ter)Affects☆☆☆☆  based on: no assertion criteria providedsingle nucleotide variant1604|CD55121909603RCV000018367NCromer blood group systemMedGen:C1292305, ...germlineGRCh381q32.2NM_001300904.2:c.261G>ANP_001287833.1:p.Trp87Ter1Aug 30,2017OMIM Allelic Variant:125240.0001c.261G>A, Affects, 0 stars, Phenotypes: Cromer blood group system, Origin: germline, 1 submittersOT1
chr1130461904130461905G>A1.130461904130461905842150411,0,Cchr1:207322483-207322484G224614|NM_000574.5(CD55):c.203G>A (p.Ser68Asn)Affects★☆☆☆  based on: criteria provided,single submittersingle nucleotide variant1604|CD55869312818RCV000210242NCromer blood group systemMedGen:C1292305, ...unknownGRCh381q32.2NM_001300904.2:c.203G>ANP_001287833.1:p.Ser68Asn1Oct 19,2015c.203G>A, Affects, 1 stars, Phenotypes: Cromer blood group system, Origin: unknown, 1 submittersOT1
chr1130461952130461953G>T1.1304619521304619535376011,0,Tchr1:207322435-207322436G787220|NM_000574.5(CD55):c.155G>T (p.Arg52Leu)Benign★☆☆☆  based on: criteria provided,single submittersingle nucleotide variant1604|CD55RCV000969421Nnot providedMedGen:CN517202germlineGRCh381q32.2NR_125349.2:n.243G>T1May 21,2018c.155G>T, Benign, 1 stars, Phenotypes: not provided, Origin: germline, 1 submittersBN1

ClinVar Lift (clinvarLift) Track Description
 

Description

This track shows human clinically relevant variants from the ClinVar database, mapped from hg38 to the mm10 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 mm10 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 mm10 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 mm10, the genome may not be G at this position. Zoom in to see the nucleotide in mm10, or click the variant to show the human position and nucleotide and the mm10 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 mm10 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 clinvarLift.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/mm10/bbi/clinvarLift.bb -chrom=chr1 -start=0 -end=100000000 stdout

Methods

The hg38 ClinvarMain track was annotated with nucleotides and positions, lifted to mm10, 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.

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