Variant Details

Variant: nssv546561

Internal ID

15207367

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr19:49618821..49856789	hg38	UCSC Ensembl
Inner	chr19:50122078..50360046	hg19	UCSC Ensembl
Inner	chr19:54813890..55051858	hg18	UCSC Ensembl

Cytoband

19q13.33

Allele length

Assembly	Allele length
hg38	237969
hg19	237969
hg18	237969

Variant Type

CNV gain

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

nsv470150

Supporting Variants

Samples

HGDP00599

Known Genes

ADM5, AP2A1, BCL2L12, CPT1C, FUZ, IRF3, MED25, MIR4749, MIR5088, MIR6799, MIR6800, PRMT1, PRR12, PTOV1, PTOV1-AS1, RRAS, SCAF1, TSKS

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

Single-copy duplication

Reference

Jakobsson_et_al_2008

Pubmed ID

18288195

Accession Number(s)

nssv546561

Frequency

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