rs5956542

chrX-123376081-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000828.5(GRIA3):c.751-18887T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.39 in 110,529 control chromosomes in the GnomAD database, including 6,550 homozygotes. There are 12,473 hemizygotes in GnomAD. 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 0.39 (6550 hom., 12473 hem., cov: 23)
• Consequence: GRIA3 NM_000828.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.200

Genes affected

GRIA3 (HGNC:4573): (glutamate ionotropic receptor AMPA type subunit 3) 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 composed of multiple subunits, arranged to form ligand-gated ion channels. The classification of glutamate receptors is based on their activation by different pharmacologic agonists. The subunit encoded by this gene belongs to a family of AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate)-sensitive glutamate receptors, and is subject to RNA editing (AGA->GGA; R->G). Alternative splicing at this locus results in different isoforms, which may vary in their signal transduction properties. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.47 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GRIA3	NM_000828.5	c.751-18887T>G		intron_variant		ENST00000622768.5
GRIA3	NM_007325.5	c.751-18887T>G		intron_variant		ENST00000620443.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GRIA3	ENST00000620443.2	c.751-18887T>G		intron_variant		1	NM_007325.5	P4
GRIA3	ENST00000622768.5	c.751-18887T>G		intron_variant		5	NM_000828.5	A1
GRIA3	ENST00000620581.4	c.751-18887T>G		intron_variant, NMD_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.390 AC: 43093 AN: 110475 Hom.: 6545 Cov.: 23 AF XY: 0.381 AC XY: 12453 AN XY: 32713

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.615

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.409

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.390 AC: 43112 AN: 110529 Hom.: 6550 Cov.: 23 AF XY: 0.381 AC XY: 12473 AN XY: 32777

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.363

Gnomad4 ASJ AF: 0.572

Gnomad4 EAS AF: 0.331

Gnomad4 SAS AF: 0.341

Gnomad4 FIN AF: 0.469

Gnomad4 NFE AF: 0.475

Gnomad4 OTH AF: 0.414

Alfa AF: 0.429 Hom.: 3565

Bravo AF: 0.380

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	7.0
Dann	Benign	0.82

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs5956542; hg19: chrX-122509932;