A curated catalogue of human genomic structural variation




Variant Details

Variant: nsv470832



Internal ID15210705
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr6:69944765..70057864hg38UCSC Ensembl
Innerchr6:70654657..70767756hg19UCSC Ensembl
Innerchr6:70711378..70824477hg18UCSC Ensembl
Cytoband6q13
Allele length
AssemblyAllele length
hg38113100
hg19113100
hg18113100
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnssv544540, nssv544542, nssv544541
SamplesHGDP00879, HGDP00863, HGDP01051
Known GenesCOL19A1
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)nsv470832
Frequency
Sample Size443
Observed Gain0
Observed Loss3
Observed Complex0
Frequencyn/a


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