rs1983812

chr9-101570761-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.780

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]

ACMG classification

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/exons	MANE	UniProt
GRIN3A	NM_133445.3	c.*2413A>G		3_prime_UTR_variant	9/9	ENST00000361820.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GRIN3A	ENST00000361820.6	c.*2413A>G		3_prime_UTR_variant	9/9	1	NM_133445.3	P1

Frequencies

GnomAD3 genomes AF: 0.492 AC: 74712 AN: 151816 Hom.: 18540 Cov.: 32

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.: 42 Cov.: 0 AF XY: 0.489 AC XY: 129 AN XY: 264

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.: 32 AF XY: 0.490 AC XY: 36332 AN XY: 74218

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	17
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

Other links and lift over

dbSNP: rs1983812; hg19: chr9-104333043;