X-123184535-C-T

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2

The NM_007325.5(GRIA3):​c.-1C>T variant causes a 5 prime UTR change. The variant allele was found at a frequency of 0.00000501 in 1,197,202 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.0000090 ( 0 hom., 0 hem., cov: 21)
Exomes 𝑓: 0.0000046 ( 0 hom. 2 hem. )

Consequence

GRIA3
NM_007325.5 5_prime_UTR

Scores

2

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 4.04
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.38).
BS2
High Hemizygotes in GnomAdExome4 at 2 XL gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GRIA3NM_000828.5 linkc.-1C>T 5_prime_UTR_variant Exon 1 of 16 ENST00000622768.5 NP_000819.4 P42263-1Q17R51
GRIA3NM_007325.5 linkc.-1C>T 5_prime_UTR_variant Exon 1 of 16 ENST00000620443.2 NP_015564.5 P42263-2Q17R51
GRIA3NM_001256743.2 linkc.-1C>T 5_prime_UTR_variant Exon 1 of 4 NP_001243672.1 Q5XKG2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GRIA3ENST00000620443 linkc.-1C>T 5_prime_UTR_variant Exon 1 of 16 1 NM_007325.5 ENSP00000478489.1 P42263-2
GRIA3ENST00000622768 linkc.-1C>T 5_prime_UTR_variant Exon 1 of 16 5 NM_000828.5 ENSP00000481554.1 P42263-1

Frequencies

GnomAD3 genomes
AF:
0.00000904
AC:
1
AN:
110612
Hom.:
0
Cov.:
21
AF XY:
0.00
AC XY:
0
AN XY:
32814
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000189
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0690
AC:
2
AN:
29
Hom.:
0
AF XY:
0.105
AC XY:
2
AN XY:
19
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0833
GnomAD4 exome
AF:
0.00000460
AC:
5
AN:
1086590
Hom.:
0
Cov.:
29
AF XY:
0.00000566
AC XY:
2
AN XY:
353162
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000601
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.00000904
AC:
1
AN:
110612
Hom.:
0
Cov.:
21
AF XY:
0.00
AC XY:
0
AN XY:
32814
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000189
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.00000756

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Uncertain:1
Jul 07, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This variant occurs in a non-coding region of the GRIA3 gene. It does not change the encoded amino acid sequence of the GRIA3 protein. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with GRIA3-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the effect of this variant on mRNA splicing is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.38
CADD
Benign
21
DANN
Benign
0.93

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs755181209; hg19: chrX-122318387; API