A curated catalogue of human genomic structural variation




Variant Details

Variant: nsv469931



Internal ID15209804
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr11:3119879..3222137hg38UCSC Ensembl
Innerchr11:3141109..3243367hg19UCSC Ensembl
Innerchr11:3097685..3199943hg18UCSC Ensembl
Cytoband11p15.4
Allele length
AssemblyAllele length
hg38102259
hg19102259
hg18102259
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnssv546060, nssv546059
SamplesHGDP00825, HGDP00882
Known GenesMRGPRG, MRGPRG-AS1, OSBPL5
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)nsv469931
Frequency
Sample Size443
Observed Gain0
Observed Loss2
Observed Complex0
Frequencyn/a


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