A curated catalogue of human genomic structural variation




Variant Details

Variant: nssv465982



Internal ID15033262
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Outerchr3:10064456..11877985hg38UCSC Ensembl
Outerchr3:10106140..11919459hg19UCSC Ensembl
Outerchr3:10081140..11894459hg18UCSC Ensembl
Cytoband3p25.2
Allele length
AssemblyAllele length
hg381813530
hg191813320
hg181813320
Variant TypeCNV insertion
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag1
Merged StatusS
Merged Variantsnsv436869
Supporting Variants
SamplesNA18505
Known GenesATG7, ATP2B2, BRK1, FANCD2, FANCD2OS, GHRL, GHRLOS, HRH1, IRAK2, LINC00606, LINC00852, MIR885, SEC13, SLC6A1, SLC6A11, SLC6A1-AS1, TAMM41, TATDN2, VGLL4, VHL
MethodSequencing
AnalysisThe best placements of paired-ends were used for identifying several different categories of SV: (i) deletions (size sd=3 kb) were identified from two or more overlapping discordant paired-ends with paired-end span >cutoff (with the condition that both putative breakpoints are spanned); (ii) simple insertions (3 kb > ssi > 2 kb) were identified from two or more overlapping discordant paired-ends with paired-end span < cutoff; (iii) mated insertions were identified from two unpaired SVs that lie in nearby (i.e. 6 kb) genomic regions and had =2 paired-ends linking to a common, distant genomic region <100 kb; mated insertions may involve tandem duplications or events related to transpositions. (iv) Inversions were called when =2 paired-ends matched different strands. (v) Unmated insertions were predicted from =2 paired ends that support a rearrangement of a genomic region in which loci change relative order without changing the relative orientation (i.e., the strand). (These events are similar to mated insertions; however, unmated insertions have only one assigned breakpoint.) In each case we required at least two paired-ends to support a predicted SV. Furthermore, at least one paired-end had to match the human reference genome at sequence identity =97%. In addition, ends were required to yield best-scoring sequence alignments genome-wide to their respective region as assessed by Blat.
Platform454
CommentsUnmated-Insertion
ReferenceKorbel_et_al_2007
Pubmed ID17901297
Accession Number(s)nssv465982
Frequency
Sample Size2
Observed Gain1
Observed Loss0
Observed Complex0
Frequencyn/a


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