rs4825847

Variant names:

• chrX-123253983-C-A
• rs4825847
• NM_000828.5:c.508+441C>A

Your query was ambiguous. Multiple possible variants found:

• chrX-123253983-C-A
• chrX-123253983-C-G
• chrX-123253983-C-T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_000828.5(GRIA3):​c.508+441C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.64 (15866 hom., 21114 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: GRIA3 NM_000828.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0160
• Publications: 2 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: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GRIA3	NM_000828.5	c.508+441C>A		intron_variant	Intron 3 of 15	ENST00000622768.5	NP_000819.4
GRIA3	NM_007325.5	c.508+441C>A		intron_variant	Intron 3 of 15	ENST00000620443.2	NP_015564.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GRIA3	ENST00000620443.2	c.508+441C>A		intron_variant	Intron 3 of 15	1	NM_007325.5	ENSP00000478489.1
GRIA3	ENST00000622768.5	c.508+441C>A		intron_variant	Intron 3 of 15	5	NM_000828.5	ENSP00000481554.1
GRIA3	ENST00000620581.4	n.508+441C>A		intron_variant	Intron 3 of 16	1		ENSP00000481875.1
ENSG00000307341	ENST00000825206.1	n.667+59862G>T		intron_variant	Intron 6 of 6

Frequencies

GnomAD3 genomes AF: 0.638 AC: 70485 AN: 110449 Hom.: 15864 Cov.: 22

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.648

Gnomad AMR AF: 0.701

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.850

Gnomad SAS AF: 0.801

Gnomad FIN AF: 0.618

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.637

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.638 AC: 70519 AN: 110503 Hom.: 15866 Cov.: 22 AF XY: 0.644 AC XY: 21114 AN XY: 32769

African (AFR) AF: 0.598 AC: 18196 AN: 30408

American (AMR) AF: 0.702 AC: 7320 AN: 10434

Ashkenazi Jewish (ASJ) AF: 0.602 AC: 1580 AN: 2624

East Asian (EAS) AF: 0.850 AC: 2946 AN: 3466

South Asian (SAS) AF: 0.801 AC: 2051 AN: 2562

European-Finnish (FIN) AF: 0.618 AC: 3645 AN: 5899

Middle Eastern (MID) AF: 0.620 AC: 134 AN: 216

European-Non Finnish (NFE) AF: 0.631 AC: 33253 AN: 52729

Other (OTH) AF: 0.642 AC: 958 AN: 1492

Alfa AF: 0.642 Hom.: 63193

Bravo AF: 0.644

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.70
PhyloP100		-0.016
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: rs4825847; hg19: chrX-122387834;