X-151963502-G-T

Variant names:

• chrX-151963502-G-T
• rs1158605
• NM_004961.4:c.343-859C>A

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_004961.4(GABRE):​c.343-859C>A 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 0.60 (14529 hom., 20294 hem., cov: 24)
  • Failed GnomAD Quality Control
• Consequence: GABRE NM_004961.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0310
• Publications: 3 publications found

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

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GABRE	NM_004961.4	c.343-859C>A		intron_variant	Intron 3 of 8	ENST00000370328.4	NP_004952.2
GABRE	XM_024452360.2	c.4-859C>A		intron_variant	Intron 4 of 9		XP_024308128.1
GABRE	XM_047441959.1	c.4-859C>A		intron_variant	Intron 3 of 8		XP_047297915.1
GABRE	XM_047441960.1	c.4-859C>A		intron_variant	Intron 2 of 8		XP_047297916.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GABRE	ENST00000370328.4	c.343-859C>A		intron_variant	Intron 3 of 8	1	NM_004961.4	ENSP00000359353.3
GABRE	ENST00000441219.5	n.*389-859C>A		intron_variant	Intron 4 of 7	2		ENSP00000389384.1
GABRE	ENST00000474932.1	n.69-859C>A		intron_variant	Intron 1 of 2	5

Frequencies

GnomAD3 genomes AF: 0.604 AC: 67013 AN: 111000 Hom.: 14526 Cov.: 24

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.597

Gnomad AMR AF: 0.723

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.558

Gnomad SAS AF: 0.703

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.672

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.625

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: 0.604 AC: 67044 AN: 111057 Hom.: 14529 Cov.: 24 AF XY: 0.609 AC XY: 20294 AN XY: 33305

African (AFR) AF: 0.440 AC: 13463 AN: 30612

American (AMR) AF: 0.724 AC: 7577 AN: 10471

Ashkenazi Jewish (ASJ) AF: 0.601 AC: 1580 AN: 2630

East Asian (EAS) AF: 0.558 AC: 1947 AN: 3492

South Asian (SAS) AF: 0.703 AC: 1849 AN: 2632

European-Finnish (FIN) AF: 0.681 AC: 4042 AN: 5938

Middle Eastern (MID) AF: 0.692 AC: 144 AN: 208

European-Non Finnish (NFE) AF: 0.664 AC: 35101 AN: 52892

Other (OTH) AF: 0.623 AC: 940 AN: 1510

Alfa AF: 0.650 Hom.: 40629

Bravo AF: 0.601

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.5
DANN	Benign	0.25
PhyloP100		-0.031
Mutation Taster		=100/0	polymorphism (auto)

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: rs1158605; hg19: chrX-151131974;