chr12-13566469-G-C

Position:

• chr12-13566469-G-C

Variant summary

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

The NM_000834.5(GRIN2B):​c.2598+556C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 152,038 control chromosomes in the GnomAD database, including 6,455 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 0.27 (6455 hom., cov: 32)
• Consequence: GRIN2B NM_000834.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.504

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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GRIN2B	NM_000834.5	c.2598+556C>G		intron_variant		ENST00000609686.4
GRIN2B	NM_001413992.1	c.2598+556C>G		intron_variant
GRIN2B	XM_005253351.3	c.384+556C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GRIN2B	ENST00000609686.4	c.2598+556C>G		intron_variant		1	NM_000834.5	P1
GRIN2B	ENST00000637214.1	c.69+42134C>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41733 AN: 151920 Hom.: 6450 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.513

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.242

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.275 AC: 41759 AN: 152038 Hom.: 6455 Cov.: 32 AF XY: 0.284 AC XY: 21126 AN XY: 74310

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.310

Gnomad4 ASJ AF: 0.389

Gnomad4 EAS AF: 0.513

Gnomad4 SAS AF: 0.460

Gnomad4 FIN AF: 0.389

Gnomad4 NFE AF: 0.302

Gnomad4 OTH AF: 0.300

Alfa AF: 0.279 Hom.: 779

Bravo AF: 0.263

Asia WGS AF: 0.472 AC: 1635 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	11
DANN	Benign	0.65

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: rs1806205; hg19: chr12-13719403;