A curated catalogue of human genomic structural variation




Variant Details

Variant: nsv470561



Internal ID15210434
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr3:50121341..50547568hg38UCSC Ensembl
Innerchr3:50158774..50584999hg19UCSC Ensembl
Innerchr3:50133778..50560003hg18UCSC Ensembl
Cytoband3p21.31
Allele length
AssemblyAllele length
hg38426228
hg19426226
hg18426226
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnssv547201, nssv547223, nssv547212
SamplesHGDP00313, HGDP00302, HGDP00697
Known GenesCACNA2D2, CYB561D2, GNAI2, GNAT1, HYAL1, HYAL2, HYAL3, IFRD2, LSMEM2, MIR5787, MIR6872, NAT6, NPRL2, RASSF1, SEMA3B, SEMA3F, SLC38A3, TMEM115, TUSC2, ZMYND10
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)nsv470561
Frequency
Sample Size443
Observed Gain0
Observed Loss3
Observed Complex0
Frequencyn/a


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