chr5:161322889:G>A Detail (hg19) (GABRA1)

Information

Genome

Assembly Position
hg19 chr5:161,322,889-161,322,889
hg38 chr5:161,895,883-161,895,883 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_000806.5:c.1059+15G>A
NM_001127644.1:c.1059+15G>A
NM_001127643.1:c.1059+15G>A
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.487
ToMMo:0.503
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.434

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 137160 OMIM
HGNC 4075 HGNC
Ensembl ENSG00000022355 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv23516857 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2013-07-03 criteria provided, multiple submitters, no conflicts not specified germline Detail
Benign 2018-01-13 criteria provided, single submitter Epilepsy, idiopathic generalized, susceptibility to, 13 germline Detail
Benign 2015-03-03 criteria provided, single submitter not provided germline Detail
Benign 2021-08-10 criteria provided, single submitter Developmental and epileptic encephalopathy, 19 germline Detail
Benign 2024-02-01 criteria provided, single submitter Epilepsy, idiopathic generalized, susceptibility to, 13,idiopathic generalized epilepsy,Epilepsy, childhood absence 4 germline Detail
Benign 2024-02-01 criteria provided, single submitter Epilepsy, idiopathic generalized, susceptibility to, 13,idiopathic generalized epilepsy,Epilepsy, childhood absence 4 germline Detail
Benign 2024-02-01 criteria provided, single submitter Epilepsy, idiopathic generalized, susceptibility to, 13,idiopathic generalized epilepsy,Epilepsy, childhood absence 4 germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.005 epilepsy We investigated the association of single-nucleotide polymorphisms in GABA(A) re... BeFree 24061200 Detail
0.003 Seizures The aim of our study was to find out the possible role of single nucleotide poly... BeFree 20356767 Detail
<0.001 epilepsy We investigated the association of single-nucleotide polymorphisms in GABA(A) re... BeFree 24061200 Detail
<0.001 epilepsy We investigated the association of single-nucleotide polymorphisms in GABA(A) re... BeFree 24061200 Detail
0.006 Seizures The aim of our study was to find out the possible role of single nucleotide poly... BeFree 20356767 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_001127644.2(GABRA1):c.1059+15G>A AND not specified ClinVar Detail
NM_001127644.2(GABRA1):c.1059+15G>A AND Epilepsy, idiopathic generalized, susceptibility to, 13 ClinVar Detail
NM_001127644.2(GABRA1):c.1059+15G>A AND not provided ClinVar Detail
NM_001127644.2(GABRA1):c.1059+15G>A AND Developmental and epileptic encephalopathy, 19 ClinVar Detail
NM_001127644.2(GABRA1):c.1059+15G>A AND multiple conditions ClinVar Detail
NM_001127644.2(GABRA1):c.1059+15G>A AND multiple conditions ClinVar Detail
NM_001127644.2(GABRA1):c.1059+15G>A AND multiple conditions ClinVar Detail
We investigated the association of single-nucleotide polymorphisms in GABA(A) receptor subunit subty... DisGeNET Detail
The aim of our study was to find out the possible role of single nucleotide polymorphisms (SNPs) pre... DisGeNET Detail
We investigated the association of single-nucleotide polymorphisms in GABA(A) receptor subunit subty... DisGeNET Detail
We investigated the association of single-nucleotide polymorphisms in GABA(A) receptor subunit subty... DisGeNET Detail
The aim of our study was to find out the possible role of single nucleotide polymorphisms (SNPs) pre... DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs2279020 dbSNP
Genome
hg19
Position
chr5:161,322,889-161,322,889
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
836
Mean of sample read depth (HGVD)
21.48
Standard deviation of sample read depth (HGVD)
11.76
Number of reference allele (HGVD)
858
Number of alternative allele (HGVD)
814
Allele Frequency (HGVD)
0.4868421052631579
Gene Symbol (HGVD)
GABRA1
ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
PASS
Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
rs2279020
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.5029
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
8428
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8616
East Asian Allele Counts (ExAC)
3737
East Asian Heterozygous Counts (ExAC)
2137
East Asian Homozygous Counts (ExAC)
800
East Asian Allele Frequency (ExAC)
0.433727948003714
Chromosome Counts in All Race (ExAC)
121316
Allele Counts in All Race (ExAC)
75111
Heterozygous Counts in All Race (ExAC)
27993
Homozygous Counts in All Race (ExAC)
23559
Allele Frequency in All Race (ExAC)
0.6191351511754426
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