rs17760877

chr12-13666539-A-C

Variant summary

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

The NM_000834.5(GRIN2B):c.1125+9206T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0937 in 152,226 control chromosomes in the GnomAD database, including 829 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 0.094 (829 hom., cov: 33)
• Consequence: GRIN2B NM_000834.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.324

Genes affected

GRIN2B (HGNC:4586): (glutamate ionotropic receptor NMDA type subunit 2B) This gene encodes a member of the N-methyl-D-aspartate (NMDA) receptor family within the ionotropic glutamate receptor superfamily. The encoded protein is a subunit of the NMDA receptor ion channel which acts as an agonist binding site for glutamate. The NMDA receptors mediate a slow calcium-permeable component of excitatory synaptic transmission in the central nervous system. The NMDA receptors are heterotetramers of seven genetically encoded, differentially expressed subunits including NR1 (GRIN1), NR2 (GRIN2A, GRIN2B, GRIN2C, or GRIN2D) and NR3 (GRIN3A or GRIN3B). The early expression of this gene in development suggests a role in brain development, circuit formation, synaptic plasticity, and cellular migration and differentiation. Naturally occurring mutations within this gene are associated with neurodevelopmental disorders including autism spectrum disorder, attention deficit hyperactivity disorder, epilepsy, and schizophrenia. [provided by RefSeq, Aug 2017]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.124 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GRIN2B	NM_000834.5	c.1125+9206T>G		intron_variant		ENST00000609686.4
GRIN2B	NM_001413992.1	c.1125+9206T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GRIN2B	ENST00000609686.4	c.1125+9206T>G		intron_variant		1	NM_000834.5	P1
GRIN2B	ENST00000630791.2	c.1125+9206T>G		intron_variant		5
GRIN2B	ENST00000636855.1	n.23+9206T>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0937 AC: 14253 AN: 152108 Hom.: 826 Cov.: 33

Gnomad AFR AF: 0.0358

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.0104

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.0937 AC: 14265 AN: 152226 Hom.: 829 Cov.: 33 AF XY: 0.0934 AC XY: 6950 AN XY: 74422

Gnomad4 AFR AF: 0.0358

Gnomad4 AMR AF: 0.129

Gnomad4 ASJ AF: 0.144

Gnomad4 EAS AF: 0.0104

Gnomad4 SAS AF: 0.110

Gnomad4 FIN AF: 0.108

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.111

Alfa AF: 0.102 Hom.: 99

Bravo AF: 0.0959

Asia WGS AF: 0.0760 AC: 264 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	5.1
Dann	Benign	0.83

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: rs17760877; hg19: chr12-13819473;