Variant chr9-101670752-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_133445.3(GRIN3A):c.1660T>C(p.Leu554=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.385 in 1,613,574 control chromosomes in the GnomAD database, including 122,987 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 0.33 ( 9450 hom., cov: 33)

Exomes 𝑓: 0.39 ( 113537 hom. )

Consequence

GRIN3A
NM_133445.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.146

Variant links:

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]

GRIN3A links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP7

Synonymous conserved (PhyloP=-0.146 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GRIN3A	NM_133445.3 linkuse as main transcript	c.1660T>C	p.Leu554=	synonymous_variant	3/9	ENST00000361820.6	NP_597702.2
GRIN3A	XM_011518211.3 linkuse as main transcript	c.1660T>C	p.Leu554=	synonymous_variant	3/7		XP_011516513.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GRIN3A	ENST00000361820.6 linkuse as main transcript	c.1660T>C	p.Leu554=	synonymous_variant	3/9	1	NM_133445.3	ENSP00000355155	P1

Frequencies

GnomAD3 genomes

AF:

0.335

AC:

50898

AN:

152020

Hom.:

9445

Cov.:

show subpopulations

Gnomad AFR

AF:

0.178

Gnomad AMI

AF:

0.331

Gnomad AMR

AF:

0.394

Gnomad ASJ

AF:

0.435

Gnomad EAS

AF:

0.214

Gnomad SAS

AF:

0.301

Gnomad FIN

AF:

0.382

Gnomad MID

AF:

0.373

Gnomad NFE

AF:

0.415

Gnomad OTH

AF:

0.364

GnomAD3 exomes

AF:

0.365

AC:

91639

AN:

251034

Hom.:

17467

AF XY:

0.368

AC XY:

49876

AN XY:

135666

show subpopulations

Gnomad AFR exome

AF:

0.172

Gnomad AMR exome

AF:

0.379

Gnomad ASJ exome

AF:

0.422

Gnomad EAS exome

AF:

0.208

Gnomad SAS exome

AF:

0.321

Gnomad FIN exome

AF:

0.391

Gnomad NFE exome

AF:

0.414

Gnomad OTH exome

AF:

0.397

GnomAD4 exome

AF:

0.390

AC:

569668

AN:

1461436

Hom.:

113537

Cov.:

AF XY:

0.389

AC XY:

282751

AN XY:

727034

show subpopulations

Gnomad4 AFR exome

AF:

0.169

Gnomad4 AMR exome

AF:

0.379

Gnomad4 ASJ exome

AF:

0.417

Gnomad4 EAS exome

AF:

0.189

Gnomad4 SAS exome

AF:

0.319

Gnomad4 FIN exome

AF:

0.388

Gnomad4 NFE exome

AF:

0.409

Gnomad4 OTH exome

AF:

0.382

GnomAD4 genome

AF:

0.335

AC:

50922

AN:

152138

Hom.:

9450

Cov.:

AF XY:

0.332

AC XY:

24683

AN XY:

74372

show subpopulations

Gnomad4 AFR

AF:

0.178

Gnomad4 AMR

AF:

0.394

Gnomad4 ASJ

AF:

0.435

Gnomad4 EAS

AF:

0.214

Gnomad4 SAS

AF:

0.302

Gnomad4 FIN

AF:

0.382

Gnomad4 NFE

AF:

0.415

Gnomad4 OTH

AF:

0.364

Alfa

AF:

0.397

Hom.:

24350

Bravo

AF:

0.329

Asia WGS

AF:

0.308

AC:

1070

AN:

3478

EpiCase

AF:

0.406

EpiControl

AF:

0.408

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.25

DANN

Benign

0.48

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over