rs10117679

Positions:

• chr9-101616197-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000361820.6(GRIN3A):​c.2615-2670G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 152,124 control chromosomes in the GnomAD database, including 2,379 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 0.13 (2379 hom., cov: 32)
• Consequence: GRIN3A ENST00000361820.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.33

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.321 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GRIN3A	NM_133445.3	c.2615-2670G>A		intron_variant		ENST00000361820.6	NP_597702.2
GRIN3A	XM_011518211.3	c.2615-2670G>A		intron_variant			XP_011516513.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GRIN3A	ENST00000361820.6	c.2615-2670G>A		intron_variant		1	NM_133445.3	ENSP00000355155	P1

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19736 AN: 152004 Hom.: 2367 Cov.: 32

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.0871

Gnomad ASJ AF: 0.0718

Gnomad EAS AF: 0.0315

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.0459

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0452

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.130 AC: 19790 AN: 152124 Hom.: 2379 Cov.: 32 AF XY: 0.128 AC XY: 9524 AN XY: 74366

Gnomad4 AFR AF: 0.325

Gnomad4 AMR AF: 0.0869

Gnomad4 ASJ AF: 0.0718

Gnomad4 EAS AF: 0.0315

Gnomad4 SAS AF: 0.112

Gnomad4 FIN AF: 0.0459

Gnomad4 NFE AF: 0.0451

Gnomad4 OTH AF: 0.117

Alfa AF: 0.0577 Hom.: 861

Bravo AF: 0.139

Asia WGS AF: 0.0910 AC: 320 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.72
DANN	Benign	0.37

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: rs10117679; hg19: chr9-104378479;