X-151955702-T-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_004961.4(GABRE):c.937+6A>T variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000062 in 1,209,983 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 29 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000080 ( 0 hom., 4 hem., cov: 24)
Exomes 𝑓: 0.000060 ( 0 hom. 25 hem. )
Consequence
GABRE
NM_004961.4 splice_donor_region, intron
NM_004961.4 splice_donor_region, intron
Scores
2
Splicing: ADA: 0.00001268
2
Clinical Significance
Conservation
PhyloP100: 0.348
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
?
Variant X-151955702-T-A is Benign according to our data. Variant chrX-151955702-T-A is described in ClinVar as [Likely_benign]. Clinvar id is 2661660.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Hemizygotes in GnomAd at 4 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GABRE | NM_004961.4 | c.937+6A>T | splice_donor_region_variant, intron_variant | ENST00000370328.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GABRE | ENST00000370328.4 | c.937+6A>T | splice_donor_region_variant, intron_variant | 1 | NM_004961.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000803 AC: 9AN: 112093Hom.: 0 Cov.: 24 AF XY: 0.000117 AC XY: 4AN XY: 34285
GnomAD3 genomes
?
AF:
AC:
9
AN:
112093
Hom.:
Cov.:
24
AF XY:
AC XY:
4
AN XY:
34285
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.0000985 AC: 18AN: 182760Hom.: 0 AF XY: 0.000149 AC XY: 10AN XY: 67256
GnomAD3 exomes
AF:
AC:
18
AN:
182760
Hom.:
AF XY:
AC XY:
10
AN XY:
67256
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0000601 AC: 66AN: 1097890Hom.: 0 Cov.: 31 AF XY: 0.0000688 AC XY: 25AN XY: 363260
GnomAD4 exome
AF:
AC:
66
AN:
1097890
Hom.:
Cov.:
31
AF XY:
AC XY:
25
AN XY:
363260
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.0000803 AC: 9AN: 112093Hom.: 0 Cov.: 24 AF XY: 0.000117 AC XY: 4AN XY: 34285
GnomAD4 genome
?
AF:
AC:
9
AN:
112093
Hom.:
Cov.:
24
AF XY:
AC XY:
4
AN XY:
34285
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2023 | GABRE: BP4, BS2 - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at