A curated catalogue of human genomic structural variation




Variant Details

Variant: nsv3382250



Internal ID19813229
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
chr5:149021872..149022029hg38UCSC Ensembl
chr5:148401435..148401592hg19UCSC Ensembl
Cytoband5q32
Allele length
AssemblyAllele length
hg38158
hg19158
Variant TypeCNV alu deletion
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnssv14666081, nssv14667577, nssv14671658, nssv14656989, nssv14653314, nssv14655288, nssv14665114
SamplesHG02106, HG00268, HG02818, HX1, HG02059, HG01352, NA19434
Known GenesSH3TC2
MethodSequencing
AnalysisRead and contig alignments were done with BLASR. The Celera assembler (8.3rc2) was used to assemble RS II samples (CHM1, CHM13, HG00514, HG00733, NA19240, HG02818, NA19434, HG01352, HG02059, NA12878, and HG04217, and Canu (1.7) was used for Sequel samples (HG02106 and HG00268). Variant calling was performed with SMRT-SV (10.1101/gr.214007.116).
PlatformPacBio RS II P6C4, PacBio Sequel v2.1
CommentsAbsence of a Alu insertion that is present in the reference
ReferenceAudano_et_al_2019
Pubmed ID30661756
Accession Number(s)nsv3382250
Frequency
Sample Size14
Observed Gain0
Observed Loss7
Observed Complex0
Frequencyn/a


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