A curated catalogue of human genomic structural variation




Variant Details

Variant: dgv1163e212



Internal ID20149619
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
chr2:109740565..110608419hg38UCSC Ensembl
chr2:110498142..111365996hg19UCSC Ensembl
Cytoband2q13
Allele length
AssemblyAllele length
hg38867855
hg19867855
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsesv3584009, esv3584008
Samples400788PV, 400113LD, 401182OC, 400829MR, 401899MB
Known GenesLIMS3, LIMS3L, LIMS3-LOC440895, LINC00116, LINC01106, LINC01123, LOC100288570, LOC100507334, LOC440895, MALL, MIR4267, MIR4436B1, MIR4436B2, NPHP1, RGPD5, RGPD6
MethodSNP array
AnalysisWe used four separate algorithms to detect CNVs; Affymetrix Chromosome Analysis Suite (ChAS), iPattern, Nexus and Partek. Our primary analysis was performed based on ChAS CNV calls, which were then supported using the remaining three algorithms to construct a confidence set of CNVs. For all algorithms, we have used 8 probes and >1kb as a base line cutoff for CNV detection.
PlatformAffymetrix CytoScan HD 2.7M array
Comments
ReferenceUddin_et_al_2014
Pubmed ID25503493
Accession Number(s)dgv1163e212
Frequency
Sample Size873
Observed Gain0
Observed Loss5
Observed Complex0
Frequencyn/a


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