A curated catalogue of human genomic structural variation




Variant Details

Variant: nsv470530



Internal ID15210403
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr2:240646778..240744491hg38UCSC Ensembl
Innerchr2:241586195..241683908hg19UCSC Ensembl
Innerchr2:241234868..241332581hg18UCSC Ensembl
Cytoband2q37.3
Allele length
AssemblyAllele length
hg3897714
hg1997714
hg1897714
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnssv547307, nssv547308
SamplesHGDP00691, HGDP01255
Known GenesAQP12A, AQP12B, KIF1A
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)nsv470530
Frequency
Sample Size443
Observed Gain2
Observed Loss0
Observed Complex0
Frequencyn/a


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