A curated catalogue of human genomic structural variation




Variant Details

Variant: nsv471069



Internal ID15210942
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr16:1754356..1791032hg38UCSC Ensembl
Innerchr16:1804357..1841033hg19UCSC Ensembl
Innerchr16:1744358..1781034hg18UCSC Ensembl
Cytoband16p13.3
Allele length
AssemblyAllele length
hg3836677
hg1936677
hg1836677
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnssv545243, nssv545239, nssv545245, nssv545240, nssv545238, nssv545241, nssv545244
SamplesHGDP00865, HGDP00962, HGDP00951, HGDP00883, HGDP00895, HGDP00894, HGDP01397
Known GenesEME2, IGFALS, MAPK8IP3, MRPS34, NME3, NUBP2, SPSB3
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)nsv471069
Frequency
Sample Size443
Observed Gain0
Observed Loss7
Observed Complex0
Frequencyn/a


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