A curated catalogue of human genomic structural variation




Variant Details

Variant: dgv1652e212



Internal ID19008860
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
chr5:140839141..140864158hg38UCSC Ensembl
chr5:140218726..140243743hg19UCSC Ensembl
Cytoband5q31.3
Allele length
AssemblyAllele length
hg3825018
hg1925018
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsesv3570466, esv3570457, esv3570464, esv3570458
Samples400238BB, 400688FL, 401962BK, 401733CG, 400047DS, 400213DB, 400599CP, 401346FJ, 400460DM, 400007RG, 400059SV, 400583HS, 400270BD, 400728PB, 401458RT, 400859SC, 400148MS, 401940SJ, 401672FD, 401919MD, 400150SS, 401151RJ, 400156WT, 401513KC, 401054VM
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
Comments
ReferenceUddin_et_al_2014
Pubmed ID25503493
Accession Number(s)dgv1652e212
Frequency
Sample Size873
Observed Gain0
Observed Loss25
Observed Complex0
Frequencyn/a


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