5-162114925-C-T

Variant summary

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

The NM_198904.4(GABRG2):​c.769+10899C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.34 in 151,464 control chromosomes in the GnomAD database, including 9,191 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 0.34 ( 9191 hom., cov: 33)

Consequence

GABRG2
NM_198904.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.863
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=-0.92).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.589 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
GABRG2NM_198904.4 linkc.769+10899C>T intron_variant ENST00000639213.2 NP_944494.1 P18507-2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
GABRG2ENST00000639213.2 linkc.769+10899C>T intron_variant 1 NM_198904.4 ENSP00000491909.2 P18507-2

Frequencies

GnomAD3 genomes
AF:
0.339
AC:
51372
AN:
151346
Hom.:
9166
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.260
Gnomad AMI
AF:
0.401
Gnomad AMR
AF:
0.396
Gnomad ASJ
AF:
0.365
Gnomad EAS
AF:
0.605
Gnomad SAS
AF:
0.480
Gnomad FIN
AF:
0.350
Gnomad MID
AF:
0.316
Gnomad NFE
AF:
0.342
Gnomad OTH
AF:
0.321
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.340
AC:
51433
AN:
151464
Hom.:
9191
Cov.:
33
AF XY:
0.344
AC XY:
25455
AN XY:
74066
show subpopulations
Gnomad4 AFR
AF:
0.260
Gnomad4 AMR
AF:
0.398
Gnomad4 ASJ
AF:
0.365
Gnomad4 EAS
AF:
0.606
Gnomad4 SAS
AF:
0.479
Gnomad4 FIN
AF:
0.350
Gnomad4 NFE
AF:
0.342
Gnomad4 OTH
AF:
0.320
Alfa
AF:
0.343
Hom.:
3797
Bravo
AF:
0.334
Asia WGS
AF:
0.540
AC:
1877
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.68
DANN
Benign
0.59

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: rs440218; hg19: chr5-161541931; API