A curated catalogue of human genomic structural variation




Variant Details

Variant: nsv470696



Internal ID15210569
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr1:12800601..12854042hg38UCSC Ensembl
Innerchr1:12860749..12913895hg19UCSC Ensembl
Innerchr1:12783336..12836482hg18UCSC Ensembl
Cytoband1p36.21
Allele length
AssemblyAllele length
hg3853442
hg1953147
hg1853147
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnssv547706, nssv547707, nssv547708, nssv547704, nssv547705
SamplesHGDP01317, HGDP00714, HGDP00560, HGDP00572, HGDP00072
Known GenesHNRNPCL1, LOC649330, PRAMEF11
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
CommentsSingle-copy duplication
ReferenceJakobsson_et_al_2008
Pubmed ID18288195
Accession Number(s)nsv470696
Frequency
Sample Size443
Observed Gain5
Observed Loss0
Observed Complex0
Frequencyn/a


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