rs3205936
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_005458.8(GABBR2):c.1587C>T(p.Leu529=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00914 in 1,605,760 control chromosomes in the GnomAD database, including 1,188 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.049 ( 651 hom., cov: 32)
Exomes 𝑓: 0.0049 ( 537 hom. )
Consequence
GABBR2
NM_005458.8 synonymous
NM_005458.8 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.363
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 -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.7).
BP6
?
Variant 9-98385715-G-A is Benign according to our data. Variant chr9-98385715-G-A is described in ClinVar as [Benign]. Clinvar id is 462125.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-0.363 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GABBR2 | NM_005458.8 | c.1587C>T | p.Leu529= | synonymous_variant | 11/19 | ENST00000259455.4 | |
GABBR2 | XM_017015331.3 | c.1293C>T | p.Leu431= | synonymous_variant | 10/18 | ||
GABBR2 | XM_005252316.6 | c.813C>T | p.Leu271= | synonymous_variant | 9/17 | ||
GABBR2 | XM_017015332.3 | c.813C>T | p.Leu271= | synonymous_variant | 8/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GABBR2 | ENST00000259455.4 | c.1587C>T | p.Leu529= | synonymous_variant | 11/19 | 1 | NM_005458.8 | P1 | |
GABBR2 | ENST00000634314.1 | n.92C>T | non_coding_transcript_exon_variant | 2/4 | 3 | ||||
GABBR2 | ENST00000637410.1 | n.1365C>T | non_coding_transcript_exon_variant | 11/19 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0495 AC: 7526AN: 152130Hom.: 652 Cov.: 32
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GnomAD3 exomes AF: 0.0124 AC: 3126AN: 251432Hom.: 246 AF XY: 0.00908 AC XY: 1234AN XY: 135890
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GnomAD4 exome AF: 0.00491 AC: 7142AN: 1453512Hom.: 537 Cov.: 27 AF XY: 0.00414 AC XY: 2998AN XY: 723668
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GnomAD4 genome ? AF: 0.0495 AC: 7529AN: 152248Hom.: 651 Cov.: 32 AF XY: 0.0472 AC XY: 3511AN XY: 74438
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Epileptic encephalopathy Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 17, 2018 | - - |
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