A curated catalogue of human genomic structural variation




Variant Details

Variant: esv13239



Internal ID11030473
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr5:140842564..140859300hg38UCSC Ensembl
Innerchr5:140222149..140238885hg19UCSC Ensembl
Innerchr5:140202333..140219069hg18UCSC Ensembl
Cytoband5q31.3
Allele length
AssemblyAllele length
hg3816737
hg1916737
hg1816737
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv26168
Supporting Variantsessv51997, essv82831, essv63870, essv53309, essv77253, essv60570, essv56868, essv36583, essv35167, essv79343, essv67206, essv50816, essv58773, essv80262, essv70128, essv68613, essv81542, essv41809, essv34613, essv62203, essv56364, essv46635, essv73406, essv40653, essv48969, essv78404, essv69168, essv38569, essv50527, essv45101, essv62948, essv72769, essv33347, essv47699, essv74319, essv65513, essv55375
SamplesNA18502, NA11995, NA18861, NA18508, NA11931, NA12004, NA19190, NA18916, NA12156, NA12044, NA12828, NA11993, NA12489, NA12878, NA18907, NA07045, NA19114, NA11894, NA12239, NA15510, NA19099, NA19257, NA19225, NA06985, NA18523, NA18858, NA19108, NA19147, NA18517, NA19240, NA07037, NA12749, NA18505, NA19129, NA12006, NA18511, NA12776
Known GenesPCDHA1, PCDHA10, PCDHA2, PCDHA3, PCDHA4, PCDHA5, PCDHA6, PCDHA7, PCDHA8, PCDHA9
MethodOligo aCGH
AnalysisSegment log2 ratios from each sample. This was done running the GADA algorithm (Pique-Regi et al., 2008) using the options "-M 10 -T 10 -a 2.5". Filter non-CNV segments using intensity thresholds. Merge remaining CNV "calls" within each sample. Adjacent calls of the same direction (gain or loss) are merged if both: the distance between calls is less than 10kb, and the distance between calls is less than 10% of the size of the largest of the two calls.
PlatformSanger H. Sapiens 42mCGH Array 5781_53 726K v1
Comments
ReferenceConrad_et_al_2009
Pubmed ID19812545
Accession Number(s)esv13239
Frequency
Sample Size40
Observed Gain37
Observed Loss0
Observed Complex0
Frequencyn/a


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