rs202183786
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 1P and 18B. PP2BP4_ModerateBP6_Very_StrongBS1BS2
The NM_001371727.1(GABRB2):c.1118G>A(p.Arg373Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000545 in 1,613,266 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R373L) has been classified as Uncertain significance.
Frequency
Consequence
NM_001371727.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GABRB2 | NM_001371727.1 | c.1118G>A | p.Arg373Gln | missense_variant | 9/10 | ENST00000393959.6 | |
GABRB2 | NM_021911.3 | c.1118G>A | p.Arg373Gln | missense_variant | 10/11 | ||
GABRB2 | NM_000813.3 | c.1077+4442G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GABRB2 | ENST00000393959.6 | c.1118G>A | p.Arg373Gln | missense_variant | 9/10 | 1 | NM_001371727.1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 151958Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000563 AC: 14AN: 248772Hom.: 0 AF XY: 0.0000594 AC XY: 8AN XY: 134690
GnomAD4 exome AF: 0.0000568 AC: 83AN: 1461308Hom.: 0 Cov.: 30 AF XY: 0.0000605 AC XY: 44AN XY: 726962
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 151958Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74196
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 26, 2021 | This variant is associated with the following publications: (PMID: 29961870) - |
Intellectual disability Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 27, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at