A curated catalogue of human genomic structural variation




Variant Details

Variant: nsv469899



Internal ID15209772
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr3:4281224..4315301hg38UCSC Ensembl
Innerchr3:4322908..4356985hg19UCSC Ensembl
Innerchr3:4297908..4331985hg18UCSC Ensembl
Cytoband3p26.1
Allele length
AssemblyAllele length
hg3834078
hg1934078
hg1834078
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnssv544920
SamplesHGDP00907
Known GenesSETMAR
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)nsv469899
Frequency
Sample Size443
Observed Gain0
Observed Loss1
Observed Complex0
Frequencyn/a


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