X-123413118-C-T

Position:

• chrX-123413118-C-T

Variant summary

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

The NM_000828.5(GRIA3):​c.1501-4284C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 110,253 control chromosomes in the GnomAD database, including 2,258 homozygotes. There are 7,159 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 0.22 (2258 hom., 7159 hem., cov: 21)
• Consequence: GRIA3 NM_000828.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0320

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GRIA3	NM_000828.5	c.1501-4284C>T		intron_variant		ENST00000622768.5	NP_000819.4
GRIA3	NM_007325.5	c.1501-4284C>T		intron_variant		ENST00000620443.2	NP_015564.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GRIA3	ENST00000620443.2	c.1501-4284C>T		intron_variant		1	NM_007325.5	ENSP00000478489	P4
GRIA3	ENST00000622768.5	c.1501-4284C>T		intron_variant		5	NM_000828.5	ENSP00000481554	A1
GRIA3	ENST00000620581.4	c.1501-4284C>T		intron_variant, NMD_transcript_variant		1		ENSP00000481875

Frequencies

GnomAD3 genomes AF: 0.223 AC: 24560 AN: 110204 Hom.: 2252 Cov.: 21 AF XY: 0.219 AC XY: 7133 AN XY: 32522

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.557

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.333

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.223 AC: 24591 AN: 110253 Hom.: 2258 Cov.: 21 AF XY: 0.220 AC XY: 7159 AN XY: 32581

Gnomad4 AFR AF: 0.254

Gnomad4 AMR AF: 0.303

Gnomad4 ASJ AF: 0.286

Gnomad4 EAS AF: 0.557

Gnomad4 SAS AF: 0.224

Gnomad4 FIN AF: 0.168

Gnomad4 NFE AF: 0.169

Gnomad4 OTH AF: 0.252

Alfa AF: 0.191 Hom.: 10218

Bravo AF: 0.247

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.0
DANN	Benign	0.38

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: rs526716; hg19: chrX-122546969;