rs2964779
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001371727.1(GABRB2):c.438C>G(p.Gly146=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00115 in 1,614,006 control chromosomes in the GnomAD database, including 20 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0054 ( 11 hom., cov: 32)
Exomes 𝑓: 0.00070 ( 9 hom. )
Consequence
GABRB2
NM_001371727.1 synonymous
NM_001371727.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.211
Genes affected
GABRB2 (HGNC:4082): (gamma-aminobutyric acid type A receptor subunit beta2) The gamma-aminobutyric acid (GABA) A receptor is a multisubunit chloride channel that mediates the fastest inhibitory synaptic transmission in the central nervous system. This gene encodes GABA A receptor, beta 2 subunit. It is mapped to chromosome 5q34 in a cluster comprised of genes encoding alpha 1 and gamma 2 subunits of the GABA A receptor. Alternative splicing of this gene generates 2 transcript variants, differing by a 114 bp insertion. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.51).
BP6
?
Variant 5-161459644-G-C is Benign according to our data. Variant chr5-161459644-G-C is described in ClinVar as [Benign]. Clinvar id is 383092.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-0.211 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00544 (829/152290) while in subpopulation AFR AF= 0.0179 (746/41570). AF 95% confidence interval is 0.0169. There are 11 homozygotes in gnomad4. There are 379 alleles in male gnomad4 subpopulation. This position pass quality control queck.
BS2
?
High AC in GnomAd at 829 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GABRB2 | NM_001371727.1 | c.438C>G | p.Gly146= | synonymous_variant | 4/10 | ENST00000393959.6 | |
GABRB2 | NM_021911.3 | c.438C>G | p.Gly146= | synonymous_variant | 5/11 | ||
GABRB2 | NM_000813.3 | c.438C>G | p.Gly146= | synonymous_variant | 5/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GABRB2 | ENST00000393959.6 | c.438C>G | p.Gly146= | synonymous_variant | 4/10 | 1 | NM_001371727.1 |
Frequencies
GnomAD3 genomes ? AF: 0.00545 AC: 829AN: 152172Hom.: 11 Cov.: 32
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GnomAD3 exomes AF: 0.00152 AC: 381AN: 251146Hom.: 5 AF XY: 0.00111 AC XY: 150AN XY: 135716
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GnomAD4 exome AF: 0.000698 AC: 1021AN: 1461716Hom.: 9 Cov.: 31 AF XY: 0.000597 AC XY: 434AN XY: 727158
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ClinVar
Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 12, 2016 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
GABRB2-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 07, 2020 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Dec 27, 2017 | - - |
Intellectual disability Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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