A curated catalogue of human genomic structural variation




Variant Details

Variant: nsv470977



Internal ID15210850
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr10:132699016..132814378hg38UCSC Ensembl
Innerchr10:134512520..134627882hg19UCSC Ensembl
Innerchr10:134362510..134477872hg18UCSC Ensembl
Cytoband10q26.3
Allele length
AssemblyAllele length
hg38115363
hg19115363
hg18115363
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnssv545015, nssv545013, nssv545012, nssv545014
SamplesHGDP00550, HGDP00825, HGDP00543, HGDP00661
Known GenesINPP5A, NKX6-2, TTC40
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)nsv470977
Frequency
Sample Size443
Observed Gain0
Observed Loss4
Observed Complex0
Frequencyn/a


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