rs707176
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BA1
The NM_000827.4(GRIA1):āc.531T>Cā(p.Ile177=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 1,613,532 control chromosomes in the GnomAD database, including 79,191 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.26 ( 5962 hom., cov: 31)
Exomes š: 0.31 ( 73229 hom. )
Consequence
GRIA1
NM_000827.4 synonymous
NM_000827.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.861
Genes affected
GRIA1 (HGNC:4571): (glutamate ionotropic receptor AMPA type subunit 1) Glutamate receptors are the predominant excitatory neurotransmitter receptors in the mammalian brain and are activated in a variety of normal neurophysiologic processes. These receptors are heteromeric protein complexes with multiple subunits, each possessing transmembrane regions, and all arranged to form a ligand-gated ion channel. The classification of glutamate receptors is based on their activation by different pharmacologic agonists. This gene belongs to a family of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate (AMPA) receptors. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.45).
BP6
?
Variant 5-153650400-T-C is Benign according to our data. Variant chr5-153650400-T-C is described in ClinVar as [Benign]. Clinvar id is 3059187.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.861 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.336 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GRIA1 | NM_000827.4 | c.531T>C | p.Ile177= | synonymous_variant | 4/16 | ENST00000285900.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GRIA1 | ENST00000285900.10 | c.531T>C | p.Ile177= | synonymous_variant | 4/16 | 1 | NM_000827.4 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.260 AC: 39500AN: 151944Hom.: 5962 Cov.: 31
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GnomAD3 exomes AF: 0.260 AC: 65161AN: 250988Hom.: 9852 AF XY: 0.260 AC XY: 35240AN XY: 135626
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GnomAD4 exome AF: 0.307 AC: 448063AN: 1461468Hom.: 73229 Cov.: 35 AF XY: 0.302 AC XY: 219935AN XY: 727068
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GnomAD4 genome ? AF: 0.260 AC: 39507AN: 152064Hom.: 5962 Cov.: 31 AF XY: 0.254 AC XY: 18894AN XY: 74324
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
GRIA1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 29, 2023 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
Benign
CADD
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DANN
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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