NM_018558.4:c.239-1100T>A

Variant names:

• chrX-152644427-T-A
• rs5925196
• NM_018558.4:c.239-1100T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018558.4(GABRQ):​c.239-1100T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 112,026 control chromosomes in the GnomAD database, including 825 homozygotes. There are 4,240 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 0.13 (825 hom., 4240 hem., cov: 24)
• Consequence: GABRQ NM_018558.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.18
• Publications: 1 publications found

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]

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018558.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GABRQ	NM_018558.4	MANE Select	c.239-1100T>A		intron	N/A	NP_061028.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GABRQ	ENST00000598523.3	TSL:1 MANE Select	c.239-1100T>A		intron	N/A	ENSP00000469332.1
	MAGEA3-DT	ENST00000671457.1		n.130-4633A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.131 AC: 14704 AN: 111971 Hom.: 825 Cov.: 24

Gnomad AFR AF: 0.0569

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.0742

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.0400

Gnomad SAS AF: 0.0787

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.131 AC: 14700 AN: 112026 Hom.: 825 Cov.: 24 AF XY: 0.124 AC XY: 4240 AN XY: 34244

African (AFR) AF: 0.0569 AC: 1756 AN: 30861

American (AMR) AF: 0.0738 AC: 785 AN: 10639

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 364 AN: 2645

East Asian (EAS) AF: 0.0398 AC: 142 AN: 3568

South Asian (SAS) AF: 0.0792 AC: 216 AN: 2726

European-Finnish (FIN) AF: 0.206 AC: 1243 AN: 6042

Middle Eastern (MID) AF: 0.195 AC: 42 AN: 215

European-Non Finnish (NFE) AF: 0.185 AC: 9809 AN: 53128

Other (OTH) AF: 0.123 AC: 188 AN: 1523

Alfa AF: 0.163 Hom.: 968

Bravo AF: 0.119

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.17
DANN	Benign	0.72
PhyloP100		-3.2

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

Other links and lift over

dbSNP: rs5925196; hg19: chrX-151812888;