rs2266856

Variant names:

• chrX-151973060-T-C
• rs2266856
• NM_004961.4:c.56+1510A>G

Your query was ambiguous. Multiple possible variants found:

• chrX-151973060-T-C
• chrX-151973060-T-G

Variant summary

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

The NM_004961.4(GABRE):​c.56+1510A>G 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 0.58 (15293 hom., 18265 hem., cov: 21)
  • Failed GnomAD Quality Control
• Consequence: GABRE NM_004961.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.987
• 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=-0.88).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004961.4. 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
	GABRE	NM_004961.4	MANE Select	c.56+1510A>G		intron	N/A	NP_004952.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GABRE	ENST00000370328.4	TSL:1 MANE Select	c.56+1510A>G		intron	N/A	ENSP00000359353.3	P78334-1
	GABRE	ENST00000417300.1	TSL:2	n.56+1510A>G		intron	N/A	ENSP00000397335.1	F2Z2H5
	GABRE	ENST00000441219.5	TSL:2	n.56+1510A>G		intron	N/A	ENSP00000389384.1	F2Z2H5

Frequencies

GnomAD3 genomes AF: 0.583 AC: 63519 AN: 108979 Hom.: 15293 Cov.: 21

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.709

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.661

Gnomad EAS AF: 0.740

Gnomad SAS AF: 0.715

Gnomad FIN AF: 0.726

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.744

Gnomad OTH AF: 0.594

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: 0.583 AC: 63536 AN: 109029 Hom.: 15293 Cov.: 21 AF XY: 0.583 AC XY: 18265 AN XY: 31355

African (AFR) AF: 0.224 AC: 6723 AN: 30031

American (AMR) AF: 0.616 AC: 6315 AN: 10256

Ashkenazi Jewish (ASJ) AF: 0.661 AC: 1728 AN: 2614

East Asian (EAS) AF: 0.740 AC: 2503 AN: 3384

South Asian (SAS) AF: 0.718 AC: 1738 AN: 2421

European-Finnish (FIN) AF: 0.726 AC: 4002 AN: 5511

Middle Eastern (MID) AF: 0.667 AC: 140 AN: 210

European-Non Finnish (NFE) AF: 0.744 AC: 39028 AN: 52451

Other (OTH) AF: 0.596 AC: 878 AN: 1473

Alfa AF: 0.628 Hom.: 20946

Bravo AF: 0.563

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.9
DANN	Benign	0.63
PhyloP100		0.99
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: rs2266856; hg19: chrX-151141532;