A curated catalogue of human genomic structural variation




Variant Details

Variant: nsv470518



Internal ID8524059
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr2:219400402..219475818hg38UCSC Ensembl
Innerchr2:220265124..220340540hg19UCSC Ensembl
Innerchr2:219973368..220048784hg18UCSC Ensembl
Cytoband2q35
Allele length
AssemblyAllele length
hg3875417
hg1975417
hg1875417
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnssv547293
SamplesHGDP00661
Known GenesDES, SPEG
MethodSNP array
AnalysisWe used the previously validated default quality control criteria, excluding samples with a log R ratio standard deviation of >0.28, a median B allele frequency of >0.55 or <0.45, or a B allele frequency drift of >0.002 (for more details see Wang et al. 2007). As the PennCNV algorithm is more sensitive and specific to CNVs covering greater numbers of SNPs in the HumanHap550 array, use of a minimum number of SNPs in CNV detection increases the reliability of CNV calls (with a consequent reduction in calls per individual). We set 10 SNPs as the minimum detection threshold in the algorithm.
PlatformIllumina HumanHap550 Genotyping BeadChip v3
Comments
ReferenceJakobsson_et_al_2008
Pubmed ID18288195
Accession Number(s)nsv470518
Frequency
Sample Size443
Observed Gain0
Observed Loss1
Observed Complex0
Frequencyn/a


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