A curated catalogue of human genomic structural variation




Variant Details

Variant: nsv470608



Internal ID15210481
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr17:78232490..78270780hg38UCSC Ensembl
Innerchr17:76228571..76266861hg19UCSC Ensembl
Innerchr17:73740166..73778456hg18UCSC Ensembl
Cytoband17q25.3
Allele length
AssemblyAllele length
hg3838291
hg1938291
hg1838291
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnssv547507, nssv547508
SamplesHGDP00978, HGDP00661
Known GenesLOC100996291, TMEM235
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)nsv470608
Frequency
Sample Size443
Observed Gain0
Observed Loss2
Observed Complex0
Frequencyn/a


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