chr9-98290275-T-TC
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_005458.8(GABBR2):c.*308_*309insG variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0056 in 138,558 control chromosomes in the GnomAD database, including 8 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0062 ( 5 hom., cov: 27)
Exomes 𝑓: 0.0013 ( 3 hom. )
Consequence
GABBR2
NM_005458.8 3_prime_UTR
NM_005458.8 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.00
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 -10 ACMG points.
BP6
?
Variant 9-98290275-T-TC is Benign according to our data. Variant chr9-98290275-T-TC is described in ClinVar as [Likely_benign]. Clinvar id is 1193790.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00617 (754/122162) while in subpopulation AFR AF= 0.0363 (713/19626). AF 95% confidence interval is 0.0341. There are 5 homozygotes in gnomad4. There are 364 alleles in male gnomad4 subpopulation. Median coverage is 27. This position pass quality control queck.
BS2
?
High AC in GnomAd at 753 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GABBR2 | NM_005458.8 | c.*308_*309insG | 3_prime_UTR_variant | 19/19 | ENST00000259455.4 | ||
GABBR2 | XM_005252316.6 | c.*308_*309insG | 3_prime_UTR_variant | 17/17 | |||
GABBR2 | XM_017015331.3 | c.*308_*309insG | 3_prime_UTR_variant | 18/18 | |||
GABBR2 | XM_017015332.3 | c.*308_*309insG | 3_prime_UTR_variant | 16/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GABBR2 | ENST00000259455.4 | c.*308_*309insG | 3_prime_UTR_variant | 19/19 | 1 | NM_005458.8 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00616 AC: 753AN: 122148Hom.: 5 Cov.: 27
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GnomAD4 exome AF: 0.00134 AC: 22AN: 16396Hom.: 3 Cov.: 0 AF XY: 0.00130 AC XY: 11AN XY: 8442
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GnomAD4 genome ? AF: 0.00617 AC: 754AN: 122162Hom.: 5 Cov.: 27 AF XY: 0.00610 AC XY: 364AN XY: 59640
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 02, 2019 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at