rs34826485
Positions:
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_000811.3(GABRA6):āc.639A>Gā(p.Gln213=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00766 in 1,613,366 control chromosomes in the GnomAD database, including 155 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.0054 ( 9 hom., cov: 32)
Exomes š: 0.0079 ( 146 hom. )
Consequence
GABRA6
NM_000811.3 synonymous
NM_000811.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.75
Genes affected
GABRA6 (HGNC:4080): (gamma-aminobutyric acid type A receptor subunit alpha6) 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. At least 16 distinct subunits of GABA-A receptors have been identified. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.55).
BP6
?
Variant 5-161689745-A-G is Benign according to our data. Variant chr5-161689745-A-G is described in ClinVar as [Benign]. Clinvar id is 477867.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=2.75 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00544 (829/152348) while in subpopulation SAS AF= 0.0381 (184/4830). AF 95% confidence interval is 0.0336. There are 9 homozygotes in gnomad4. There are 408 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 9 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GABRA6 | NM_000811.3 | c.639A>G | p.Gln213= | synonymous_variant | 6/9 | ENST00000274545.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GABRA6 | ENST00000274545.10 | c.639A>G | p.Gln213= | synonymous_variant | 6/9 | 1 | NM_000811.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00545 AC: 829AN: 152230Hom.: 8 Cov.: 32
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GnomAD3 exomes AF: 0.00934 AC: 2347AN: 251216Hom.: 39 AF XY: 0.0116 AC XY: 1570AN XY: 135826
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GnomAD4 exome AF: 0.00789 AC: 11524AN: 1461018Hom.: 146 Cov.: 31 AF XY: 0.00914 AC XY: 6644AN XY: 726878
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GnomAD4 genome ? AF: 0.00544 AC: 829AN: 152348Hom.: 9 Cov.: 32 AF XY: 0.00548 AC XY: 408AN XY: 74502
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Childhood absence epilepsy Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 26, 2019 | - - |
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