rs763017992
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_005458.8(GABBR2):c.1668G>A(p.Arg556=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000939 in 1,596,872 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000066 ( 1 hom., cov: 33)
Exomes 𝑓: 0.0000035 ( 0 hom. )
Consequence
GABBR2
NM_005458.8 synonymous
NM_005458.8 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.441
Genes affected
GABBR2 (HGNC:4507): (gamma-aminobutyric acid type B receptor subunit 2) The multi-pass membrane protein encoded by this gene belongs to the G-protein coupled receptor 3 family and GABA-B receptor subfamily. The GABA-B receptors inhibit neuronal activity through G protein-coupled second-messenger systems, which regulate the release of neurotransmitters, and the activity of ion channels and adenylyl cyclase. This receptor subunit forms an active heterodimeric complex with GABA-B receptor subunit 1, neither of which is effective on its own. Allelic variants of this gene have been associated with nicotine dependence.[provided by RefSeq, Jan 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.33).
BP6
?
Variant 9-98371566-C-T is Benign according to our data. Variant chr9-98371566-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 462126.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.441 with no splicing effect.
BS2
?
High AC in GnomAd4 at 10 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GABBR2 | NM_005458.8 | c.1668G>A | p.Arg556= | synonymous_variant | 12/19 | ENST00000259455.4 | |
GABBR2 | XM_017015331.3 | c.1374G>A | p.Arg458= | synonymous_variant | 11/18 | ||
GABBR2 | XM_005252316.6 | c.894G>A | p.Arg298= | synonymous_variant | 10/17 | ||
GABBR2 | XM_017015332.3 | c.894G>A | p.Arg298= | synonymous_variant | 9/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GABBR2 | ENST00000259455.4 | c.1668G>A | p.Arg556= | synonymous_variant | 12/19 | 1 | NM_005458.8 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000657 AC: 10AN: 152108Hom.: 1 Cov.: 33
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GnomAD4 exome AF: 0.00000346 AC: 5AN: 1444764Hom.: 0 Cov.: 26 AF XY: 0.00 AC XY: 0AN XY: 720060
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GnomAD4 genome ? AF: 0.0000657 AC: 10AN: 152108Hom.: 1 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74290
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Epileptic encephalopathy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 27, 2023 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at