dbSNP rs1983812: GRIN3A:c.*2413A>G (chr9-101570761-T-C) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_133445.3(GRIN3A):c.*2413A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.492 in 152,370 control chromosomes in the GnomAD database, including 18,592 homozygotes. 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 0.49 ( 18550 hom., cov: 32)

Exomes 𝑓: 0.46 ( 42 hom. )

Consequence

GRIN3A
NM_133445.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.780

Variant links:

Genes affected

GRIN3A (HGNC:16767): (glutamate ionotropic receptor NMDA type subunit 3A) This gene encodes a subunit of the N-methyl-D-aspartate (NMDA) receptors, which belong to the superfamily of glutamate-regulated ion channels, and function in physiological and pathological processes in the central nervous system. This subunit shows greater than 90% identity to the corresponding subunit in rat. Studies in the knockout mouse deficient in this subunit suggest that this gene may be involved in the development of synaptic elements by modulating NMDA receptor activity. [provided by RefSeq, Jul 2008]

GRIN3A links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.45).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.647 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GRIN3A	NM_133445.3 link	c.*2413A>G		3_prime_UTR_variant	Exon 9 of 9	ENST00000361820.6	NP_597702.2	Q8TCU5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GRIN3A	ENST00000361820 link	c.*2413A>G		3_prime_UTR_variant	Exon 9 of 9	1	NM_133445.3	ENSP00000355155.3		Q8TCU5

Frequencies

GnomAD3 genomes

AF:

0.492

AC:

74712

AN:

151816

Hom.:

18540

Cov.:

show subpopulations

Gnomad AFR

AF:

0.463

Gnomad AMI

AF:

0.473

Gnomad AMR

AF:

0.494

Gnomad ASJ

AF:

0.472

Gnomad EAS

AF:

0.665

Gnomad SAS

AF:

0.564

Gnomad FIN

AF:

0.456

Gnomad MID

AF:

0.446

Gnomad NFE

AF:

0.498

Gnomad OTH

AF:

0.504

GnomAD4 exome

AF:

0.463

AC:

202

AN:

436

Hom.:

Cov.:

AF XY:

0.489

AC XY:

129

AN XY:

264

show subpopulations

Gnomad4 FIN exome

AF:

0.469

Gnomad4 NFE exome

AF:

0.167

Gnomad4 OTH exome

AF:

0.250

GnomAD4 genome

AF:

0.492

AC:

74772

AN:

151934

Hom.:

18550

Cov.:

AF XY:

0.490

AC XY:

36332

AN XY:

74218

show subpopulations

Gnomad4 AFR

AF:

0.464

Gnomad4 AMR

AF:

0.494

Gnomad4 ASJ

AF:

0.472

Gnomad4 EAS

AF:

0.666

Gnomad4 SAS

AF:

0.564

Gnomad4 FIN

AF:

0.456

Gnomad4 NFE

AF:

0.498

Gnomad4 OTH

AF:

0.501

Alfa

AF:

0.497

Hom.:

38507

Bravo

AF:

0.492

Asia WGS

AF:

0.638

AC:

2214

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.45

CADD

Benign

DANN

Benign

0.81

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over