A curated catalogue of human genomic structural variation




Variant Details

Variant: nsv470049



Internal ID15209922
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr4:85829546..85855335hg38UCSC Ensembl
Innerchr4:86750699..86776488hg19UCSC Ensembl
Innerchr4:86969723..86995512hg18UCSC Ensembl
Cytoband4q21.23
Allele length
AssemblyAllele length
hg3825790
hg1925790
hg1825790
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnssv546330
SamplesHGDP00675
Known GenesARHGAP24
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)nsv470049
Frequency
Sample Size443
Observed Gain0
Observed Loss1
Observed Complex0
Frequencyn/a


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