NM_133445.3:c.*2413A>G

Variant names:

• chr9-101570761-T-C
• rs1983812
• NM_133445.3:c.*2413A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 15 publications found

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

Our verdict: Benign. The variant received -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	c.*2413A>G		3_prime_UTR_variant	Exon 9 of 9	ENST00000361820.6	NP_597702.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GRIN3A	ENST00000361820.6	c.*2413A>G		3_prime_UTR_variant	Exon 9 of 9	1	NM_133445.3	ENSP00000355155.3

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.469 AC: 200 AN: 426

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.167 AC: 1 AN: 6

Other (OTH) AF: 0.250 AC: 1 AN: 4

GnomAD4 genome AF: 0.492 AC: 74772 AN: 151934 Hom.: 18550 Cov.: 32 AF XY: 0.490 AC XY: 36332 AN XY: 74218

African (AFR) AF: 0.464 AC: 19197 AN: 41416

American (AMR) AF: 0.494 AC: 7543 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.472 AC: 1639 AN: 3472

East Asian (EAS) AF: 0.666 AC: 3430 AN: 5154

South Asian (SAS) AF: 0.564 AC: 2715 AN: 4818

European-Finnish (FIN) AF: 0.456 AC: 4813 AN: 10544

Middle Eastern (MID) AF: 0.452 AC: 132 AN: 292

European-Non Finnish (NFE) AF: 0.498 AC: 33815 AN: 67946

Other (OTH) AF: 0.501 AC: 1057 AN: 2110

Alfa AF: 0.494 Hom.: 78796

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
PhyloP100		0.78
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1983812; hg19: chr9-104333043;