rs1337697

Variant names:

• chr9-101716645-C-G
• rs1337697
• NM_133445.3:c.699+20636G>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.699+20636G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.425 in 151,534 control chromosomes in the GnomAD database, including 13,853 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 0.43 (13853 hom., cov: 32)
• Consequence: GRIN3A NM_133445.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.632
• Publications: 3 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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.461 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GRIN3A	NM_133445.3	c.699+20636G>C		intron_variant	Intron 1 of 8	ENST00000361820.6	NP_597702.2
GRIN3A	XM_011518211.3	c.699+20636G>C		intron_variant	Intron 1 of 6		XP_011516513.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GRIN3A	ENST00000361820.6	c.699+20636G>C		intron_variant	Intron 1 of 8	1	NM_133445.3	ENSP00000355155.3

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64419 AN: 151416 Hom.: 13848 Cov.: 32

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.425 AC: 64443 AN: 151534 Hom.: 13853 Cov.: 32 AF XY: 0.428 AC XY: 31660 AN XY: 74018

African (AFR) AF: 0.338 AC: 13955 AN: 41346

American (AMR) AF: 0.457 AC: 6953 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.417 AC: 1445 AN: 3464

East Asian (EAS) AF: 0.381 AC: 1956 AN: 5138

South Asian (SAS) AF: 0.460 AC: 2213 AN: 4810

European-Finnish (FIN) AF: 0.465 AC: 4863 AN: 10458

Middle Eastern (MID) AF: 0.432 AC: 126 AN: 292

European-Non Finnish (NFE) AF: 0.465 AC: 31556 AN: 67794

Other (OTH) AF: 0.433 AC: 910 AN: 2104

Alfa AF: 0.442 Hom.: 1797

Bravo AF: 0.423

Asia WGS AF: 0.388 AC: 1353 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.4
DANN	Benign	0.33
PhyloP100		-0.63
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: rs1337697; hg19: chr9-104478927;