A curated catalogue of human genomic structural variation




Variant Details

Variant: nsv470259



Internal ID15210132
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr12:1798687..1835876hg38UCSC Ensembl
Innerchr12:1907853..1945042hg19UCSC Ensembl
Innerchr12:1778114..1815303hg18UCSC Ensembl
Cytoband12p13.33
Allele length
AssemblyAllele length
hg3837190
hg1937190
hg1837190
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnssv546870
SamplesHGDP00657
Known GenesCACNA2D4, LRTM2
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)nsv470259
Frequency
Sample Size443
Observed Gain0
Observed Loss1
Observed Complex0
Frequencyn/a


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