A curated catalogue of human genomic structural variation




Variant Details

Variant: nsv470809



Internal ID8524350
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr6:31529138..31576412hg38UCSC Ensembl
Innerchr6:31496915..31544189hg19UCSC Ensembl
Innerchr6:31604894..31652168hg18UCSC Ensembl
Cytoband6p21.33
Allele length
AssemblyAllele length
hg3847275
hg1947275
hg1847275
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnssv544475
SamplesHGDP00697
Known GenesATP6V1G2, ATP6V1G2-DDX39B, DDX39B, LTA, MCCD1, NFKBIL1, SNORD117, SNORD84, TNF
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)nsv470809
Frequency
Sample Size443
Observed Gain0
Observed Loss1
Observed Complex0
Frequencyn/a


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