A curated catalogue of human genomic structural variation




Variant Details

Variant: esv3570459



Internal ID18351971
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr5:140839141..140852165hg38UCSC Ensembl
Innerchr5:140218726..140231750hg19UCSC Ensembl
Cytoband5q31.3
Allele length
AssemblyAllele length
hg3813025
hg1913025
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsdgv1651e212
Supporting Variantsessv9776282, essv9776280, essv9776283, essv9776281, essv9776279, essv9776278, essv9776276
Samples401162TM, 401634CH, 401908YM, 401496SL, 401881TJ, 400863SS, 401735LE
Known GenesPCDHA1, PCDHA2, PCDHA3, PCDHA4, PCDHA5, PCDHA6, PCDHA7, PCDHA8, PCDHA9
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)esv3570459
Frequency
Sample Size873
Observed Gain0
Observed Loss7
Observed Complex0
Frequencyn/a


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