rs1139916
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_004961.4(GABRE):āc.304T>Gā(p.Ser102Ala) variant causes a missense change. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Genomes: š 0.64 ( 16408 hom., 20676 hem., cov: 22)
Exomes š: 0.70 ( 178081 hom. 253983 hem. )
Failed GnomAD Quality Control
Consequence
GABRE
NM_004961.4 missense
NM_004961.4 missense
Scores
3
13
Clinical Significance
Conservation
PhyloP100: 4.11
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]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=1.0047327E-4).
BP6
?
Variant X-151969707-A-C is Benign according to our data. Variant chrX-151969707-A-C is described in ClinVar as [Benign]. Clinvar id is 1280403.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GABRE | NM_004961.4 | c.304T>G | p.Ser102Ala | missense_variant | 3/9 | ENST00000370328.4 | |
GABRE | XM_024452360.2 | c.-36T>G | 5_prime_UTR_variant | 4/10 | |||
GABRE | XM_047441959.1 | c.-36T>G | 5_prime_UTR_variant | 3/9 | |||
GABRE | XM_047441960.1 | c.-36T>G | 5_prime_UTR_variant | 2/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GABRE | ENST00000370328.4 | c.304T>G | p.Ser102Ala | missense_variant | 3/9 | 1 | NM_004961.4 | P1 | |
GABRE | ENST00000465405.1 | n.398T>G | non_coding_transcript_exon_variant | 2/2 | 1 | ||||
GABRE | ENST00000474932.1 | n.30T>G | non_coding_transcript_exon_variant | 1/3 | 5 | ||||
GABRE | ENST00000441219.5 | c.*350T>G | 3_prime_UTR_variant, NMD_transcript_variant | 4/8 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.644 AC: 70536AN: 109473Hom.: 16409 Cov.: 22 AF XY: 0.650 AC XY: 20649AN XY: 31775
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GnomAD3 exomes AF: 0.716 AC: 130407AN: 182165Hom.: 29673 AF XY: 0.726 AC XY: 48429AN XY: 66681
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GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.696 AC: 763144AN: 1096589Hom.: 178081 Cov.: 33 AF XY: 0.701 AC XY: 253983AN XY: 362189
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GnomAD4 genome ? Data not reliable, filtered out with message: InbreedingCoeff AF: 0.644 AC: 70564AN: 109531Hom.: 16408 Cov.: 22 AF XY: 0.649 AC XY: 20676AN XY: 31843
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Data not reliable, filtered out with message: InbreedingCoeff
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 14, 2020 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M
MutationTaster
Benign
P;P;P
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Uncertain
D
Sift4G
Benign
T
Polyphen
P
Vest4
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at