Variant Details

Variant: nssv547223

Internal ID

15207919

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr3:50201579..50547568	hg38	UCSC Ensembl
Inner	chr3:50239012..50584999	hg19	UCSC Ensembl
Inner	chr3:50214016..50560003	hg18	UCSC Ensembl

Cytoband

3p21.31

Allele length

Assembly	Allele length
hg38	345990
hg19	345988
hg18	345988

Variant Type

CNV loss

Copy Number

Allele State

Heterozygous

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

nsv470561

Supporting Variants

Samples

HGDP00697

Known Genes

CACNA2D2, CYB561D2, GNAI2, HYAL1, HYAL2, HYAL3, IFRD2, LSMEM2, MIR5787, MIR6872, NAT6, NPRL2, RASSF1, SEMA3B, SLC38A3, TMEM115, TUSC2, ZMYND10

Method

SNP array

Analysis

We 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.

Platform

Illumina HumanHap550 Genotyping BeadChip v3

Comments

Reference

Jakobsson_et_al_2008

Pubmed ID

18288195

Accession Number(s)

nssv547223

Frequency

Sample Size	443
Observed Gain	0
Observed Loss	1
Observed Complex	0
Frequency	n/a