A curated catalogue of human genomic structural variation




Variant Details

Variant: esv3570596



Internal ID18352108
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr5:179804973..179813403hg38UCSC Ensembl
Innerchr5:179231973..179240403hg19UCSC Ensembl
Cytoband5q35.3
Allele length
AssemblyAllele length
hg388431
hg198431
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsessv9777007, essv9777006, essv9777008, essv9777005, essv9777004
Samples401734PG, 401672FD, 400763BT, 400248JO, 401012TP
Known GenesMGAT4B, SQSTM1
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)esv3570596
Frequency
Sample Size873
Observed Gain0
Observed Loss5
Observed Complex0
Frequencyn/a


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