A curated catalogue of human genomic structural variation




Variant Details

Variant: essv9775154



Internal ID18294863
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr5:69551239..71358232hg38UCSC Ensembl
Innerchr5:68847066..70654059hg19UCSC Ensembl
Cytoband5q13.2
Allele length
AssemblyAllele length
hg381806994
hg191806994
Variant TypeCNV loss
Copy Number1
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusS
Merged Variantsesv3570183
Supporting Variants
Samples400444MM
Known GenesGTF2H2, GTF2H2B, GTF2H2C, GTF2H2D, GUSBP3, GUSBP9, LOC100272216, LOC441081, LOC647859, NAIP, OCLN, SERF1A, SERF1B, SMA4, SMA5, SMN1, SMN2
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=14
ReferenceUddin_et_al_2014
Pubmed ID25503493
Accession Number(s)essv9775154
Frequency
Sample Size873
Observed Gain0
Observed Loss1
Observed Complex0
Frequencyn/a


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