rs1003794

chrX-151966832-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004961.4(GABRE):c.342+2837C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 111,197 control chromosomes in the GnomAD database, including 4,901 homozygotes. There are 11,121 hemizygotes in GnomAD. 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 0.35 (4901 hom., 11121 hem., cov: 24)
• Consequence: GABRE NM_004961.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.51

Genes affected

GABRE (HGNC:4085): (gamma-aminobutyric acid type A receptor subunit epsilon) The product of this gene belongs to the ligand-gated ionic channel (TC 1.A.9) family. It encodes the gamma-aminobutyric acid (GABA) A receptor which is a multisubunit chloride channel that mediates the fastest inhibitory synaptic transmission in the central nervous system. This gene encodes an epsilon subunit. It is mapped to chromosome Xq28 in a cluster comprised of genes encoding alpha 3, beta 4 and theta subunits of the same receptor. Alternatively spliced transcript variants have been identified, but only one is thought to encode a protein. [provided by RefSeq, Oct 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GABRE	NM_004961.4	c.342+2837C>G		intron_variant		ENST00000370328.4
GABRE	XM_024452360.2	c.3+2837C>G		intron_variant
GABRE	XM_047441959.1	c.3+2837C>G		intron_variant
GABRE	XM_047441960.1	c.3+2837C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GABRE	ENST00000370328.4	c.342+2837C>G		intron_variant		1	NM_004961.4	P1
GABRE	ENST00000441219.5	c.*388+2837C>G		intron_variant, NMD_transcript_variant		2
GABRE	ENST00000474932.1	n.68+2837C>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.347 AC: 38536 AN: 111140 Hom.: 4907 Cov.: 24 AF XY: 0.333 AC XY: 11092 AN XY: 33352

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.290

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.347 AC: 38540 AN: 111197 Hom.: 4901 Cov.: 24 AF XY: 0.333 AC XY: 11121 AN XY: 33419

Gnomad4 AFR AF: 0.346

Gnomad4 AMR AF: 0.271

Gnomad4 ASJ AF: 0.401

Gnomad4 EAS AF: 0.437

Gnomad4 SAS AF: 0.286

Gnomad4 FIN AF: 0.362

Gnomad4 NFE AF: 0.357

Gnomad4 OTH AF: 0.343

Alfa AF: 0.353 Hom.: 2299

Bravo AF: 0.345

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	4.5
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

Other links and lift over

dbSNP: rs1003794; hg19: chrX-151135304;