chr5-162088209-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_198904.4(GABRG2):​c.108-5619C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 152,038 control chromosomes in the GnomAD database, including 1,028 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.11 ( 1028 hom., cov: 32)

Consequence

GABRG2
NM_198904.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.634
Variant links:
Genes affected
GABRG2 (HGNC:4087): (gamma-aminobutyric acid type A receptor subunit gamma2) This gene encodes a gamma-aminobutyric acid (GABA) receptor. GABA is the major inhibitory neurotransmitter in the mammlian brain, where it acts at GABA-A receptors, which are ligand-gated chloride channels. GABA-A receptors are pentameric, consisting of proteins from several subunit classes: alpha, beta, gamma, delta and rho. Mutations in this gene have been associated with epilepsy and febrile seizures. Multiple transcript variants encoding different isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.133 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
GABRG2NM_198904.4 linkuse as main transcriptc.108-5619C>T intron_variant ENST00000639213.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
GABRG2ENST00000639213.2 linkuse as main transcriptc.108-5619C>T intron_variant 1 NM_198904.4 A1P18507-2

Frequencies

GnomAD3 genomes
AF:
0.112
AC:
17050
AN:
151920
Hom.:
1029
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0857
Gnomad AMI
AF:
0.128
Gnomad AMR
AF:
0.0888
Gnomad ASJ
AF:
0.131
Gnomad EAS
AF:
0.0777
Gnomad SAS
AF:
0.132
Gnomad FIN
AF:
0.0979
Gnomad MID
AF:
0.155
Gnomad NFE
AF:
0.135
Gnomad OTH
AF:
0.120
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.112
AC:
17058
AN:
152038
Hom.:
1028
Cov.:
32
AF XY:
0.110
AC XY:
8209
AN XY:
74294
show subpopulations
Gnomad4 AFR
AF:
0.0855
Gnomad4 AMR
AF:
0.0886
Gnomad4 ASJ
AF:
0.131
Gnomad4 EAS
AF:
0.0777
Gnomad4 SAS
AF:
0.132
Gnomad4 FIN
AF:
0.0979
Gnomad4 NFE
AF:
0.135
Gnomad4 OTH
AF:
0.121
Alfa
AF:
0.132
Hom.:
1833
Bravo
AF:
0.111
Asia WGS
AF:
0.114
AC:
397
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.27
DANN
Benign
0.48

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2268582; hg19: chr5-161515215; COSMIC: COSV62716375; API