A curated catalogue of human genomic structural variation




Variant Details

Variant: nsv470901



Internal ID15210774
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr21:43361476..43464372hg38UCSC Ensembl
Innerchr21:44781356..44884252hg19UCSC Ensembl
Innerchr21:43605784..43708680hg18UCSC Ensembl
Cytoband21q22.3
Allele length
AssemblyAllele length
hg38102897
hg19102897
hg18102897
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnssv544783, nssv544784, nssv544782
SamplesHGDP00546, HGDP00978, HGDP00661
Known GenesLINC00313, LINC00319, SIK1
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)nsv470901
Frequency
Sample Size443
Observed Gain0
Observed Loss3
Observed Complex0
Frequencyn/a


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