rs10117679

Variant names:

• chr9-101616197-C-T
• rs10117679
• NM_133445.3:c.2615-2670G>A

Variant summary

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

The NM_133445.3(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 NM_133445.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.33
• Publications: 2 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=-0.91).
• 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 rank	MANE	Protein	UniProt
GRIN3A	NM_133445.3	c.2615-2670G>A		intron_variant	Intron 5 of 8	ENST00000361820.6	NP_597702.2
GRIN3A	XM_011518211.3	c.2615-2670G>A		intron_variant	Intron 5 of 6		XP_011516513.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GRIN3A	ENST00000361820.6	c.2615-2670G>A		intron_variant	Intron 5 of 8	1	NM_133445.3	ENSP00000355155.3
ENSG00000299588	ENST00000764873.1	n.223+9822C>T		intron_variant	Intron 2 of 4
ENSG00000299588	ENST00000764875.1	n.198+9822C>T		intron_variant	Intron 2 of 3

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

African (AFR) AF: 0.325 AC: 13483 AN: 41464

American (AMR) AF: 0.0869 AC: 1330 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0718 AC: 249 AN: 3470

East Asian (EAS) AF: 0.0315 AC: 163 AN: 5168

South Asian (SAS) AF: 0.112 AC: 537 AN: 4814

European-Finnish (FIN) AF: 0.0459 AC: 486 AN: 10592

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.0451 AC: 3069 AN: 68000

Other (OTH) AF: 0.117 AC: 246 AN: 2110

Alfa AF: 0.0715 Hom.: 3275

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
PhyloP100		-2.3
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: rs10117679; hg19: chr9-104378479;