A curated catalogue of human genomic structural variation




Variant Details

Variant: nsv470046



Internal ID15209919
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr4:70296786..70402393hg38UCSC Ensembl
Innerchr4:71162503..71268110hg19UCSC Ensembl
Innerchr4:71197092..71302699hg18UCSC Ensembl
Cytoband4q13.3
Allele length
AssemblyAllele length
hg38105608
hg19105608
hg18105608
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnssv546327
SamplesHGDP00615
Known GenesCABS1, PROL1, SMR3A, SMR3B
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)nsv470046
Frequency
Sample Size443
Observed Gain0
Observed Loss1
Observed Complex0
Frequencyn/a


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