chr9-101655272-C-A

Variant names:

• chr9-101655272-C-A
• rs1323421
• NM_133445.3:c.2352+14788G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_133445.3(GRIN3A):​c.2352+14788G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.473 in 151,544 control chromosomes in the GnomAD database, including 17,161 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 0.47 (17161 hom., cov: 32)
• Consequence: GRIN3A NM_133445.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.73
• Publications: 6 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]

ENSG00000299588 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GRIN3A	NM_133445.3	c.2352+14788G>T		intron_variant	Intron 3 of 8	ENST00000361820.6	NP_597702.2
GRIN3A	XM_011518211.3	c.2352+14788G>T		intron_variant	Intron 3 of 6		XP_011516513.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GRIN3A	ENST00000361820.6	c.2352+14788G>T		intron_variant	Intron 3 of 8	1	NM_133445.3	ENSP00000355155.3

Frequencies

GnomAD3 genomes AF: 0.473 AC: 71639 AN: 151426 Hom.: 17139 Cov.: 32

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.495

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.473 AC: 71708 AN: 151544 Hom.: 17161 Cov.: 32 AF XY: 0.471 AC XY: 34860 AN XY: 74056

African (AFR) AF: 0.472 AC: 19534 AN: 41376

American (AMR) AF: 0.495 AC: 7519 AN: 15178

Ashkenazi Jewish (ASJ) AF: 0.525 AC: 1817 AN: 3458

East Asian (EAS) AF: 0.267 AC: 1365 AN: 5112

South Asian (SAS) AF: 0.409 AC: 1967 AN: 4814

European-Finnish (FIN) AF: 0.483 AC: 5094 AN: 10546

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.483 AC: 32710 AN: 67750

Other (OTH) AF: 0.497 AC: 1047 AN: 2106

Alfa AF: 0.482 Hom.: 9890

Bravo AF: 0.472

Asia WGS AF: 0.413 AC: 1439 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	16
DANN	Benign	0.51
PhyloP100		2.7
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: rs1323421; hg19: chr9-104417554;