A curated catalogue of human genomic structural variation




Variant Details

Variant: nsv436983



Internal ID8349383
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr5:96776022..96776301hg38UCSC Ensembl
Outerchr5:96774507..96776379hg38UCSC Ensembl
Innerchr5:96111726..96112005hg19UCSC Ensembl
Outerchr5:96110211..96112083hg19UCSC Ensembl
Innerchr5:96137482..96137761hg18UCSC Ensembl
Outerchr5:96135967..96137839hg18UCSC Ensembl
Innerchr5:96185799..96186078hg16UCSC Ensembl
Outerchr5:96184284..96186156hg16UCSC Ensembl
Cytoband5q15
Allele length
AssemblyAllele length
hg381873
hg191873
hg181873
hg161873
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnssv466864
SamplesNA10847
Known GenesCAST, ERAP1
MethodSNP array
AnalysisOur algorithm aims to detect deletions that are transmitted from a hemizygous parent to a child. For each trio, every SNP was coded into one of seven categories: (A) Type I mendelian incompatibility (that is, consistent with deletion) involving mother; (B) Type I mendelian incompatibility involving father; (C) Type II mendelian incompatibility (that is, inconsistent with deletion); (D) child homozygous or missing data, both parents homozygous or missing data; (E) child homozygous or missing data, father heterozygous, mother homozygous or missing data; (F) child homozygous or missing data, mother heterozygous, father homozygous or missing data; (G) child heterozygous or both parents heterozygous (see Supplementary Methods for further details). SNPs were assigned to states D-G only if they did not contain mendelian incompatibilities. A run of consecutive SNPs in a particular trio was considered to be consistent with a maternal transmitted deletion if all SNPs were in states A, D or E, or with a paternal deletion if all SNPs were in states B, D or F.
PlatformNot reported
Comments
ReferenceConrad_et_al_2006
Pubmed ID16327808
Accession Number(s)nsv436983
Frequency
Sample Size60
Observed Gain0
Observed Loss1
Observed Complex0
Frequencyn/a


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