A curated catalogue of human genomic structural variation




Variant Details

Variant: nsv470204



Internal ID15210077
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr8:22094715..22171155hg38UCSC Ensembl
Innerchr8:21952226..22028668hg19UCSC Ensembl
Innerchr8:22008172..22084613hg18UCSC Ensembl
Cytoband8p21.3
Allele length
AssemblyAllele length
hg3876441
hg1976443
hg1876442
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnssv546715, nssv546714, nssv546712, nssv546713
SamplesHGDP00550, HGDP00963, HGDP00960, HGDP00657
Known GenesBMP1, FAM160B2, HR, LGI3, NUDT18, REEP4, SFTPC
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)nsv470204
Frequency
Sample Size443
Observed Gain0
Observed Loss4
Observed Complex0
Frequencyn/a


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