rs12658835
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Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1
The NM_001127644.2(GABRA1):c.-142A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 151,944 control chromosomes in the GnomAD database, including 3,307 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.19 ( 3304 hom., cov: 30)
Exomes 𝑓: 0.17 ( 3 hom. )
Consequence
GABRA1
NM_001127644.2 5_prime_UTR
NM_001127644.2 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.05
Genes affected
GABRA1 (HGNC:4075): (gamma-aminobutyric acid type A receptor subunit alpha1) This gene encodes a gamma-aminobutyric acid (GABA) receptor. GABA is the major inhibitory neurotransmitter in the mammalian brain where it acts at GABA-A receptors, which are ligand-gated chloride channels. Chloride conductance of these channels can be modulated by agents such as benzodiazepines that bind to the GABA-A receptor. GABA-A receptors are pentameric, consisting of proteins from several subunit classes: alpha, beta, gamma, delta and rho. Mutations in this gene cause juvenile myoclonic epilepsy and childhood absence epilepsy type 4. Multiple transcript variants encoding the same protein have been identified for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -18 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.41).
BP6
?
Variant 5-161848296-A-G is Benign according to our data. Variant chr5-161848296-A-G is described in ClinVar as [Benign]. Clinvar id is 352592.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GABRA1 | NM_001127644.2 | c.-142A>G | 5_prime_UTR_variant | 1/10 | ENST00000393943.10 | ||
LOC105377696 | XR_941158.4 | n.74+2224T>C | intron_variant, non_coding_transcript_variant | ||||
GABRA1 | NM_000806.5 | c.-142A>G | 5_prime_UTR_variant | 2/11 | |||
GABRA1 | NM_001127643.2 | c.-142A>G | 5_prime_UTR_variant | 2/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GABRA1 | ENST00000393943.10 | c.-142A>G | 5_prime_UTR_variant | 1/10 | 1 | NM_001127644.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.187 AC: 28318AN: 151656Hom.: 3301 Cov.: 30
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GnomAD4 exome AF: 0.169 AC: 29AN: 172Hom.: 3 Cov.: 0 AF XY: 0.184 AC XY: 21AN XY: 114
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GnomAD4 genome ? AF: 0.187 AC: 28328AN: 151772Hom.: 3304 Cov.: 30 AF XY: 0.190 AC XY: 14096AN XY: 74150
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Epilepsy, idiopathic generalized, susceptibility to, 13 Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 23, 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