A curated catalogue of human genomic structural variation




Variant Details

Variant: nsv470583



Internal ID8524124
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr3:53145738..53200978hg38UCSC Ensembl
Innerchr3:53179754..53234994hg19UCSC Ensembl
Innerchr3:53154794..53210034hg18UCSC Ensembl
Cytoband3p21.1
Allele length
AssemblyAllele length
hg3855241
hg1955241
hg1855241
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnssv547246
SamplesHGDP00546
Known GenesPRKCD
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)nsv470583
Frequency
Sample Size443
Observed Gain0
Observed Loss1
Observed Complex0
Frequencyn/a


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