chrX-123459038-A-G

Variant names:

• chrX-123459038-A-G
• rs557762
• NM_000828.5:c.2077-5827A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000828.5(GRIA3):​c.2077-5827A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.339 in 110,751 control chromosomes in the GnomAD database, including 5,830 homozygotes. There are 10,822 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 0.34 (5830 hom., 10822 hem., cov: 23)
• Consequence: GRIA3 NM_000828.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.957
• Publications: 3 publications found

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]

GRIA3 Gene-Disease associations (from GenCC):

• syndromic X-linked intellectual disability 94

  Inheritance: XL Classification: DEFINITIVE, STRONG, LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), G2P
• X-linked complex neurodevelopmental disorder

  Inheritance: XL Classification: DEFINITIVE Submitted by: ClinGen
• X-linked intellectual disability due to GRIA3 anomalies

  Inheritance: XL Classification: SUPPORTIVE Submitted by: Orphanet

ENSG00000307341 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.602 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000828.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GRIA3	NM_000828.5	MANE Plus Clinical	c.2077-5827A>G		intron	N/A	NP_000819.4
	GRIA3	NM_007325.5	MANE Select	c.2077-5827A>G		intron	N/A	NP_015564.5

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GRIA3	ENST00000620443.2	TSL:1 MANE Select	c.2077-5827A>G		intron	N/A	ENSP00000478489.1
	GRIA3	ENST00000622768.5	TSL:5 MANE Plus Clinical	c.2077-5827A>G		intron	N/A	ENSP00000481554.1
	GRIA3	ENST00000620581.4	TSL:1	n.2077-5827A>G		intron	N/A	ENSP00000481875.1

Frequencies

GnomAD3 genomes AF: 0.339 AC: 37548 AN: 110706 Hom.: 5831 Cov.: 23

Gnomad AFR AF: 0.609

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.261

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.347

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

GnomAD4 genome AF: 0.339 AC: 37579 AN: 110751 Hom.: 5830 Cov.: 23 AF XY: 0.328 AC XY: 10822 AN XY: 33029

African (AFR) AF: 0.609 AC: 18516 AN: 30388

American (AMR) AF: 0.380 AC: 3959 AN: 10409

Ashkenazi Jewish (ASJ) AF: 0.240 AC: 633 AN: 2640

East Asian (EAS) AF: 0.236 AC: 831 AN: 3518

South Asian (SAS) AF: 0.185 AC: 493 AN: 2666

European-Finnish (FIN) AF: 0.251 AC: 1476 AN: 5880

Middle Eastern (MID) AF: 0.277 AC: 59 AN: 213

European-Non Finnish (NFE) AF: 0.206 AC: 10867 AN: 52855

Other (OTH) AF: 0.344 AC: 518 AN: 1507

Alfa AF: 0.256 Hom.: 13554

Bravo AF: 0.368

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.23
DANN	Benign	0.54
PhyloP100		-0.96
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs557762; hg19: chrX-122592889;