Variant Details

Variant: nsv817828

Internal ID

16059983

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr2:46443007..46512018	hg38	UCSC Ensembl
Inner	chr2:46670146..46739157	hg19	UCSC Ensembl
Inner	chr2:46523650..46592661	hg18	UCSC Ensembl
Inner	chr2:46581797..46650808	hg17	UCSC Ensembl

Cytoband

2p21

Allele length

Assembly	Allele length
hg38	69012
hg19	69012
hg18	69012
hg17	69012

Variant Type

CNV loss

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

Supporting Variants

nssv1418345, nssv1418346

Samples

NA12146, NA10847

Known Genes

ATP6V1E2, TMEM247

Method

SNP array

Analysis

An integrated HMM algorithm was developed and we constructed accurate models for log R Ratio and B Allele Frequency. We developed more realistic models for state transition between different copy number states. PennCNV incorporates the population allele frequency for each SNP and the distance between adjacent SNPs. We incorporated a Bayesian approach into PennCNV to use family information for a posteriori CNV validation and CNV boundary mapping.

Platform

GPL6433

Comments

Reference

Wang_et_al_2007

Pubmed ID

17921354

Accession Number(s)

nsv817828

Frequency

Sample Size	112
Observed Gain	0
Observed Loss	2
Observed Complex	0
Frequency	n/a