rs201116009
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The NM_005458.8(GABBR2):c.2660+10T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000572 in 1,354,464 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 Benign (★).
Frequency
Genomes: 𝑓 0.00058 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00057 ( 1 hom. )
Consequence
GABBR2
NM_005458.8 intron
NM_005458.8 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.29
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 -8 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.39).
BP6
?
Variant 9-98293775-A-C is Benign according to our data. Variant chr9-98293775-A-C is described in ClinVar as [Benign]. Clinvar id is 462135.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High AC in GnomAd4 at 89 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GABBR2 | NM_005458.8 | c.2660+10T>G | intron_variant | ENST00000259455.4 | |||
GABBR2 | XM_005252316.6 | c.1886+10T>G | intron_variant | ||||
GABBR2 | XM_017015331.3 | c.2366+10T>G | intron_variant | ||||
GABBR2 | XM_017015332.3 | c.1886+10T>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GABBR2 | ENST00000259455.4 | c.2660+10T>G | intron_variant | 1 | NM_005458.8 | P1 | |||
GABBR2 | ENST00000637410.1 | n.2438+10T>G | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000585 AC: 89AN: 152244Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000649 AC: 158AN: 243370Hom.: 0 AF XY: 0.000617 AC XY: 81AN XY: 131376
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GnomAD4 exome AF: 0.000571 AC: 686AN: 1202102Hom.: 1 Cov.: 16 AF XY: 0.000561 AC XY: 342AN XY: 609454
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GnomAD4 genome ? AF: 0.000584 AC: 89AN: 152362Hom.: 0 Cov.: 33 AF XY: 0.000470 AC XY: 35AN XY: 74514
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Epileptic encephalopathy Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
Computational scores
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Name
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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