A curated catalogue of human genomic structural variation




Variant Details

Variant: nsv470252



Internal ID15210125
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr12:84652..194154hg38UCSC Ensembl
Innerchr12:193818..303320hg19UCSC Ensembl
Innerchr12:64079..173581hg18UCSC Ensembl
Cytoband12p13.33
Allele length
AssemblyAllele length
hg38109503
hg19109503
hg18109503
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnssv546862, nssv546863
SamplesHGDP00903, HGDP00894
Known GenesIQSEC3, LOC574538, SLC6A12
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)nsv470252
Frequency
Sample Size443
Observed Gain2
Observed Loss0
Observed Complex0
Frequencyn/a


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