A curated catalogue of human genomic structural variation




Variant Details

Variant: nsv471257



Internal ID15211130
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr15:84869224..84919085hg38UCSC Ensembl
Innerchr15:85412455..85462316hg19UCSC Ensembl
Innerchr15:83213459..83263320hg18UCSC Ensembl
Cytoband15q25.3
Allele length
AssemblyAllele length
hg3849862
hg1949862
hg1849862
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnssv545748, nssv545749
SamplesHGDP00562, HGDP00564
Known GenesALPK3, SLC28A1
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)nsv471257
Frequency
Sample Size443
Observed Gain2
Observed Loss0
Observed Complex0
Frequencyn/a


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