Variant Details

Variant: esv34078

Internal ID

12624955

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr5:161443467..161931704	hg38	UCSC Ensembl
Inner	chr5:160870473..161358710	hg19	UCSC Ensembl
Inner	chr5:160803051..161291288	hg18	UCSC Ensembl

Cytoband

5q34

Allele length

Assembly	Allele length
hg38	488238
hg19	488238
hg18	488238

Variant Type

CNV loss

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

Supporting Variants

essv6990670

Samples

Known Genes

GABRA1, GABRA6, GABRB2

Method

SNP array

Analysis

We further explored the discovery of segmental deletions in the Kosraean population data where IBD is more prevalent, and we observe a larger number of gaps.We used a binomial score to rank potential deletions in homozygous gaps based on the number of mismatching SNPs and the rate of mismatch in the flanking shared segments, measured across all shared segments with the suspected gap. To prioritize the segmental gaps that were most likely to be representative of a deletion, we developed a scoring function based on the number of mismatching SNPs and levels of homozygosity in the gap.

Platform

Not reported

Comments

Reference

Gusev_et_al_2009

Pubmed ID

18971310

Accession Number(s)

esv34078

Frequency

Sample Size	270
Observed Gain	0
Observed Loss	0
Observed Complex	0
Frequency	n/a