chrX-123232086-C-A

Position:

• chrX-123232086-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_000828.5(GRIA3):​c.269-21217C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0174 in 111,508 control chromosomes in the GnomAD database, including 24 homozygotes. There are 517 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 0.017 (24 hom., 517 hem., cov: 23)
• Consequence: GRIA3 NM_000828.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.103

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=-0.78).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0174 (1940/111508) while in subpopulation NFE AF= 0.0266 (1412/53026). AF 95% confidence interval is 0.0255. There are 24 homozygotes in gnomad4. There are 517 alleles in male gnomad4 subpopulation. Median coverage is 23. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 24 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GRIA3	NM_000828.5	c.269-21217C>A		intron_variant		ENST00000622768.5	NP_000819.4
GRIA3	NM_007325.5	c.269-21217C>A		intron_variant		ENST00000620443.2	NP_015564.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GRIA3	ENST00000620443.2	c.269-21217C>A		intron_variant		1	NM_007325.5	ENSP00000478489	P4
GRIA3	ENST00000622768.5	c.269-21217C>A		intron_variant		5	NM_000828.5	ENSP00000481554	A1
GRIA3	ENST00000620581.4	c.269-21217C>A		intron_variant, NMD_transcript_variant		1		ENSP00000481875
GRIA3	ENST00000479118.1	n.245-21217C>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0174 AC: 1939 AN: 111454 Hom.: 23 Cov.: 23 AF XY: 0.0153 AC XY: 518 AN XY: 33758

Gnomad AFR AF: 0.00378

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0121

Gnomad ASJ AF: 0.0167

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00114

Gnomad FIN AF: 0.0344

Gnomad MID AF: 0.00847

Gnomad NFE AF: 0.0266

Gnomad OTH AF: 0.0187

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

GnomAD4 genome AF: 0.0174 AC: 1940 AN: 111508 Hom.: 24 Cov.: 23 AF XY: 0.0153 AC XY: 517 AN XY: 33822

Gnomad4 AFR AF: 0.00378

Gnomad4 AMR AF: 0.0122

Gnomad4 ASJ AF: 0.0167

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00114

Gnomad4 FIN AF: 0.0344

Gnomad4 NFE AF: 0.0266

Gnomad4 OTH AF: 0.0184

Alfa AF: 0.0250 Hom.: 133

Bravo AF: 0.0155

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	1.7
DANN	Benign	0.65

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: rs5911556; hg19: chrX-122365937;