A curated catalogue of human genomic structural variation




Variant Details

Variant: nsv471227



Internal ID15211100
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr7:2589386..2729230hg38UCSC Ensembl
Innerchr7:2629020..2768864hg19UCSC Ensembl
Innerchr7:2595546..2735390hg18UCSC Ensembl
Cytoband7p22.2
Allele length
AssemblyAllele length
hg38139845
hg19139845
hg18139845
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnssv544954, nssv544998, nssv544976, nssv544965, nssv544987
SamplesHGDP00789, HGDP00302, HGDP00543, HGDP01412, HGDP00661
Known GenesAMZ1, GNA12, IQCE, TTYH3
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)nsv471227
Frequency
Sample Size443
Observed Gain0
Observed Loss5
Observed Complex0
Frequencyn/a


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