A curated catalogue of human genomic structural variation




Variant Details

Variant: nsv470620



Internal ID15210493
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr17:81516973..82064485hg38UCSC Ensembl
Innerchr17:79483999..80022361hg19UCSC Ensembl
Innerchr17:77098594..77615650hg18UCSC Ensembl
Cytoband17q25.3
Allele length
AssemblyAllele length
hg38547513
hg19538363
hg18517057
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnssv547542, nssv547536, nssv547541, nssv547539, nssv547540, nssv547537, nssv547538
SamplesHGDP00789, HGDP00702, HGDP00550, HGDP00825, HGDP00978, HGDP00657, HGDP00661
Known GenesALYREF, ANAPC11, ARHGDIA, ARL16, ASPSCR1, C17orf70, CCDC137, DCXR, DUS1L, FAM195B, FSCN2, GCGR, GPS1, HGS, LRRC45, MAFG, MAFG-AS1, MIR6786, MRPL12, MYADML2, NOTUM, NPB, NPLOC4, OXLD1, P4HB, PCYT2, PDE6G, PPP1R27, PYCR1, RAC3, RFNG, SIRT7, SLC25A10, STRA13, TSPAN10
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)nsv470620
Frequency
Sample Size443
Observed Gain0
Observed Loss7
Observed Complex0
Frequencyn/a


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