A curated catalogue of human genomic structural variation

Variant Details

Variant: nsv470012

Internal ID15209885
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr4:8169674..8231614hg38UCSC Ensembl
Innerchr4:8171401..8233341hg19UCSC Ensembl
Innerchr4:8222301..8284241hg18UCSC Ensembl
Allele length
AssemblyAllele length
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnssv546271, nssv546272, nssv546270
SamplesHGDP00302, HGDP00825, HGDP00543
Known GenesSH3TC1
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
Pubmed ID18288195
Accession Number(s)nsv470012
Sample Size443
Observed Gain0
Observed Loss3
Observed Complex0

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