NM_133445.3:c.1304+4020T>C

Variant names:

• chr9-101682576-A-G
• rs1572560
• NM_133445.3:c.1304+4020T>C

Variant summary

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

The NM_133445.3(GRIN3A):​c.1304+4020T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.791 in 152,216 control chromosomes in the GnomAD database, including 48,046 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 0.79 (48046 hom., cov: 34)
• Consequence: GRIN3A NM_133445.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.854
• Publications: 0 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.86 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GRIN3A	NM_133445.3	c.1304+4020T>C		intron_variant	Intron 2 of 8	ENST00000361820.6	NP_597702.2
GRIN3A	XM_011518211.3	c.1304+4020T>C		intron_variant	Intron 2 of 6		XP_011516513.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GRIN3A	ENST00000361820.6	c.1304+4020T>C		intron_variant	Intron 2 of 8	1	NM_133445.3	ENSP00000355155.3

Frequencies

GnomAD3 genomes AF: 0.790 AC: 120217 AN: 152098 Hom.: 47991 Cov.: 34

Gnomad AFR AF: 0.867

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.743

Gnomad ASJ AF: 0.795

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.751

Gnomad FIN AF: 0.806

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.783

Gnomad OTH AF: 0.776

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

GnomAD4 genome AF: 0.791 AC: 120335 AN: 152216 Hom.: 48046 Cov.: 34 AF XY: 0.789 AC XY: 58718 AN XY: 74428

African (AFR) AF: 0.867 AC: 36026 AN: 41530

American (AMR) AF: 0.743 AC: 11358 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.795 AC: 2760 AN: 3472

East Asian (EAS) AF: 0.439 AC: 2267 AN: 5168

South Asian (SAS) AF: 0.752 AC: 3631 AN: 4828

European-Finnish (FIN) AF: 0.806 AC: 8542 AN: 10592

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.783 AC: 53241 AN: 68022

Other (OTH) AF: 0.780 AC: 1644 AN: 2108

Alfa AF: 0.788 Hom.: 23188

Bravo AF: 0.783

Asia WGS AF: 0.615 AC: 2141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.85
DANN	Benign	0.36
PhyloP100		-0.85
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: rs1572560; hg19: chr9-104444858;