rs5958198

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_000828.5(GRIA3):​c.269-22192A>C 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 0.57 ( 13446 hom., 19110 hem., cov: 22)
Failed GnomAD Quality Control

Consequence

GRIA3
NM_000828.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.08
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 -4 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.78).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
GRIA3NM_000828.5 linkuse as main transcriptc.269-22192A>C intron_variant ENST00000622768.5
GRIA3NM_007325.5 linkuse as main transcriptc.269-22192A>C intron_variant ENST00000620443.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
GRIA3ENST00000620443.2 linkuse as main transcriptc.269-22192A>C intron_variant 1 NM_007325.5 P4P42263-2
GRIA3ENST00000622768.5 linkuse as main transcriptc.269-22192A>C intron_variant 5 NM_000828.5 A1P42263-1
GRIA3ENST00000620581.4 linkuse as main transcriptc.269-22192A>C intron_variant, NMD_transcript_variant 1
GRIA3ENST00000479118.1 linkuse as main transcriptn.245-22192A>C intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.573
AC:
63253
AN:
110480
Hom.:
13445
Cov.:
22
AF XY:
0.582
AC XY:
19093
AN XY:
32808
show subpopulations
Gnomad AFR
AF:
0.365
Gnomad AMI
AF:
0.481
Gnomad AMR
AF:
0.721
Gnomad ASJ
AF:
0.618
Gnomad EAS
AF:
0.967
Gnomad SAS
AF:
0.772
Gnomad FIN
AF:
0.603
Gnomad MID
AF:
0.643
Gnomad NFE
AF:
0.622
Gnomad OTH
AF:
0.597
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:
0.572
AC:
63267
AN:
110532
Hom.:
13446
Cov.:
22
AF XY:
0.581
AC XY:
19110
AN XY:
32870
show subpopulations
Gnomad4 AFR
AF:
0.364
Gnomad4 AMR
AF:
0.722
Gnomad4 ASJ
AF:
0.618
Gnomad4 EAS
AF:
0.967
Gnomad4 SAS
AF:
0.772
Gnomad4 FIN
AF:
0.603
Gnomad4 NFE
AF:
0.622
Gnomad4 OTH
AF:
0.602
Alfa
AF:
0.626
Hom.:
68398
Bravo
AF:
0.577

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.78
CADD
Benign
13
DANN
Benign
0.78

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: rs5958198; hg19: chrX-122364962; API