Variant X-152649545-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_018558.4(GABRQ):c.611-197T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.55 ( 12279 hom., 17922 hem., cov: 23)

Failed GnomAD Quality Control

Consequence

GABRQ
NM_018558.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0250

Variant links:

Genes affected

GABRQ (HGNC:14454): (gamma-aminobutyric acid type A receptor subunit theta) The gamma-aminobutyric acid (GABA) A receptor is a multisubunit chloride channel that mediates the fastest inhibitory synaptic transmission in the central nervous system. This gene encodes the theta subunit of the GABA A receptor. The gene is mapped to chromosome Xq28 in a cluster of genes including those that encode the alpha 3 and epsilon subunits of the GABA A receptor. [provided by RefSeq, Jul 2017]

GABRQ links:

MAGEA3-DT (HGNC:56247): (MAGEA3 divergent transcript)

MAGEA3-DT links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GABRQ	NM_018558.4 linkuse as main transcript	c.611-197T>C		intron_variant		ENST00000598523.3
MAGEA3-DT	XR_938525.3 linkuse as main transcript	n.157-9751A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GABRQ	ENST00000598523.3 linkuse as main transcript	c.611-197T>C		intron_variant		1	NM_018558.4	P1
MAGEA3-DT	ENST00000671457.1 linkuse as main transcript	n.130-9751A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.547

AC:

60505

AN:

110540

Hom.:

12283

Cov.:

AF XY:

0.545

AC XY:

17870

AN XY:

32816

show subpopulations

Gnomad AFR

AF:

0.724

Gnomad AMI

AF:

0.539

Gnomad AMR

AF:

0.395

Gnomad ASJ

AF:

0.413

Gnomad EAS

AF:

0.658

Gnomad SAS

AF:

0.569

Gnomad FIN

AF:

0.509

Gnomad MID

AF:

0.500

Gnomad NFE

AF:

0.480

Gnomad OTH

AF:

0.529

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.547

AC:

60542

AN:

110596

Hom.:

12279

Cov.:

AF XY:

0.545

AC XY:

17922

AN XY:

32880

show subpopulations

Gnomad4 AFR

AF:

0.725

Gnomad4 AMR

AF:

0.395

Gnomad4 ASJ

AF:

0.413

Gnomad4 EAS

AF:

0.658

Gnomad4 SAS

AF:

0.567

Gnomad4 FIN

AF:

0.509

Gnomad4 NFE

AF:

0.480

Gnomad4 OTH

AF:

0.529

Alfa

AF:

0.480

Hom.:

16895

Bravo

AF:

0.549

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.54

Splicing

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over