A curated catalogue of human genomic structural variation




Variant Details

Variant: nsv470124



Internal ID15209997
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr19:10289228..10362257hg38UCSC Ensembl
Innerchr19:10399904..10472933hg19UCSC Ensembl
Innerchr19:10260904..10333933hg18UCSC Ensembl
Cytoband19p13.2
Allele length
AssemblyAllele length
hg3873030
hg1973030
hg1873030
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnssv546457, nssv546456
SamplesHGDP00893, HGDP01090
Known GenesFDX1L, ICAM3, ICAM5, RAVER1, TYK2, ZGLP1
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)nsv470124
Frequency
Sample Size443
Observed Gain2
Observed Loss0
Observed Complex0
Frequencyn/a


Hosted by The Centre for Applied Genomics
Grant support for DGV
Please read the usage disclaimer