A curated catalogue of human genomic structural variation




Variant Details

Variant: nsv470103



Internal ID15209976
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr19:1086044..1325151hg38UCSC Ensembl
Innerchr19:1086043..1325150hg19UCSC Ensembl
Innerchr19:1037043..1276150hg18UCSC Ensembl
Cytoband19p13.3
Allele length
AssemblyAllele length
hg38239108
hg19239108
hg18239108
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnssv546418, nssv546416, nssv546417
SamplesHGDP00553, HGDP00925, HGDP00938
Known GenesATP5D, C19orf24, C19orf26, CIRBP, CIRBP-AS1, EFNA2, GPX4, HMHA1, MIDN, POLR2E, SBNO2, STK11
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)nsv470103
Frequency
Sample Size443
Observed Gain3
Observed Loss0
Observed Complex0
Frequencyn/a


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