A curated catalogue of human genomic structural variation




Variant Details

Variant: nsv470296



Internal ID8523837
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr12:57718406..57783509hg38UCSC Ensembl
Innerchr12:58112189..58177292hg19UCSC Ensembl
Innerchr12:56398456..56463559hg18UCSC Ensembl
Cytoband12q14.1
Allele length
AssemblyAllele length
hg3865104
hg1965104
hg1865104
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnssv546948
SamplesHGDP01412
Known GenesAGAP2, AGAP2-AS1, CDK4, CYP27B1, MARCH9, METTL1, METTL21B, MIR6759, OS9, TSFM, TSPAN31
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)nsv470296
Frequency
Sample Size443
Observed Gain0
Observed Loss1
Observed Complex0
Frequencyn/a


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