1-2019509-G-A
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_000815.5(GABRD):c.68+18G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000383 in 704,402 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0012 ( 0 hom., cov: 29)
Exomes 𝑓: 0.00018 ( 1 hom. )
Consequence
GABRD
NM_000815.5 intron
NM_000815.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.441
Genes affected
GABRD (HGNC:4084): (gamma-aminobutyric acid type A receptor subunit delta) Gamma-aminobutyric acid (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. The GABA-A receptor is generally pentameric and there are five types of subunits: alpha, beta, gamma, delta, and rho. This gene encodes the delta subunit. Mutations in this gene have been associated with susceptibility to generalized epilepsy with febrile seizures, type 5. Alternatively spliced transcript variants have been described for this gene, but their biological validity has not been determined. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BP6
Variant 1-2019509-G-A is Benign according to our data. Variant chr1-2019509-G-A is described in ClinVar as [Benign]. Clinvar id is 1608248.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GABRD | NM_000815.5 | c.68+18G>A | intron_variant | ENST00000378585.7 | NP_000806.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GABRD | ENST00000378585.7 | c.68+18G>A | intron_variant | 1 | NM_000815.5 | ENSP00000367848.4 |
Frequencies
GnomAD3 genomes AF: 0.00115 AC: 169AN: 146366Hom.: 0 Cov.: 29
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GnomAD4 exome AF: 0.000181 AC: 101AN: 557926Hom.: 1 Cov.: 6 AF XY: 0.000178 AC XY: 47AN XY: 263890
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GnomAD4 genome AF: 0.00115 AC: 169AN: 146476Hom.: 0 Cov.: 29 AF XY: 0.000952 AC XY: 68AN XY: 71444
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Idiopathic generalized epilepsy Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 15, 2024 | - - |
Computational scores
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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