X-152649545-T-C

Variant names:

• chrX-152649545-T-C
• rs5924753
• NM_018558.4:c.611-197T>C

Variant summary

Our verdict is Likely benign. The variant received -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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0250
• Publications: 4 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: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GABRQ	NM_018558.4	MANE Select	c.611-197T>C		intron	N/A	NP_061028.3	Q9UN88

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GABRQ	ENST00000598523.3	TSL:1 MANE Select	c.611-197T>C		intron	N/A	ENSP00000469332.1	Q9UN88
	MAGEA3-DT	ENST00000671457.1		n.130-9751A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.547 AC: 60505 AN: 110540 Hom.: 12283 Cov.: 23

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.: 23 AF XY: 0.545 AC XY: 17922 AN XY: 32880

African (AFR) AF: 0.725 AC: 21988 AN: 30340

American (AMR) AF: 0.395 AC: 4150 AN: 10514

Ashkenazi Jewish (ASJ) AF: 0.413 AC: 1085 AN: 2629

East Asian (EAS) AF: 0.658 AC: 2275 AN: 3460

South Asian (SAS) AF: 0.567 AC: 1475 AN: 2601

European-Finnish (FIN) AF: 0.509 AC: 2985 AN: 5866

Middle Eastern (MID) AF: 0.493 AC: 106 AN: 215

European-Non Finnish (NFE) AF: 0.480 AC: 25313 AN: 52780

Other (OTH) AF: 0.529 AC: 803 AN: 1519

Alfa AF: 0.493 Hom.: 25292

Bravo AF: 0.549

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.54
PhyloP100		-0.025

Splicing

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

Other links and lift over

dbSNP: rs5924753; hg19: chrX-151818008;