rs3734201
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002042.5(GABRR1):c.*46A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.418 in 1,500,802 control chromosomes in the GnomAD database, including 133,001 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.42 ( 13673 hom., cov: 32)
Exomes 𝑓: 0.42 ( 119328 hom. )
Consequence
GABRR1
NM_002042.5 3_prime_UTR
NM_002042.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0770
Genes affected
GABRR1 (HGNC:4090): (gamma-aminobutyric acid type A receptor subunit rho1) GABA is the major inhibitory neurotransmitter in the mammalian brain where it acts at GABA receptors, which are ligand-gated chloride channels. GABRR1 is a member of the rho subunit family. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GABRR1 | NM_002042.5 | c.*46A>G | 3_prime_UTR_variant | 10/10 | ENST00000454853.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GABRR1 | ENST00000454853.7 | c.*46A>G | 3_prime_UTR_variant | 10/10 | 1 | NM_002042.5 | P1 | ||
GABRR1 | ENST00000369451.7 | c.*46A>G | 3_prime_UTR_variant | 12/12 | 5 | ||||
GABRR1 | ENST00000435811.5 | c.*46A>G | 3_prime_UTR_variant | 9/9 | 2 | ||||
GABRR1 | ENST00000457434.1 | downstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.421 AC: 63891AN: 151850Hom.: 13641 Cov.: 32
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GnomAD3 exomes AF: 0.411 AC: 100920AN: 245522Hom.: 21282 AF XY: 0.411 AC XY: 54722AN XY: 132996
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GnomAD4 exome AF: 0.417 AC: 563083AN: 1348834Hom.: 119328 Cov.: 20 AF XY: 0.418 AC XY: 281996AN XY: 675040
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GnomAD4 genome ? AF: 0.421 AC: 63977AN: 151968Hom.: 13673 Cov.: 32 AF XY: 0.411 AC XY: 30557AN XY: 74282
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at