A curated catalogue of human genomic structural variation




Variant Details

Variant: essv9776292



Internal ID18284318
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr5:140839141..140863096hg38UCSC Ensembl
Innerchr5:140218726..140242681hg19UCSC Ensembl
Cytoband5q31.3
Allele length
AssemblyAllele length
hg3823956
hg1923956
Variant TypeCNV loss
Copy Number1
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusS
Merged Variantsesv3570458
Supporting Variants
Samples400150SS
Known GenesPCDHA1, PCDHA10, 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
CommentsNumber of probes=15
ReferenceUddin_et_al_2014
Pubmed ID25503493
Accession Number(s)essv9776292
Frequency
Sample Size873
Observed Gain0
Observed Loss1
Observed Complex0
Frequencyn/a


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