A curated catalogue of human genomic structural variation




Variant Details

Variant: nsv471057



Internal ID15210930
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr5:177310308..177469411hg38UCSC Ensembl
Innerchr5:176737309..176896412hg19UCSC Ensembl
Innerchr5:176669915..176829018hg18UCSC Ensembl
Cytoband5q35.3
Allele length
AssemblyAllele length
hg38159104
hg19159104
hg18159104
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnssv545183, nssv545182
SamplesHGDP00288, HGDP00546
Known GenesDBN1, F12, GRK6, LMAN2, MXD3, PFN3, PRR7, PRR7-AS1, RGS14, SLC34A1
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)nsv471057
Frequency
Sample Size443
Observed Gain0
Observed Loss2
Observed Complex0
Frequencyn/a


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