dbSNP rs1337676: GRIN3A:c.-360C>T (chr9-101738339-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_133445.3(GRIN3A):c.-360C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.466 in 313,056 control chromosomes in the GnomAD database, including 34,785 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 0.45 ( 15845 hom., cov: 34)

Exomes 𝑓: 0.48 ( 18940 hom. )

Consequence

GRIN3A
NM_133445.3 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.10

Publications

4 publications found

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:

ENSG00000299588 (HGNC:):

ENSG00000299588 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.493 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GRIN3A	NM_133445.3 link	c.-360C>T		5_prime_UTR_variant	Exon 1 of 9	ENST00000361820.6	NP_597702.2	Q8TCU5
GRIN3A	XM_011518211.3 link	c.-360C>T		5_prime_UTR_variant	Exon 1 of 7		XP_011516513.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GRIN3A	ENST00000361820.6 link	c.-360C>T		5_prime_UTR_variant	Exon 1 of 9	1	NM_133445.3	ENSP00000355155.3		Q8TCU5

Frequencies

GnomAD3 genomes

AF:

0.453

AC:

68816

AN:

152042

Hom.:

15837

Cov.:

show subpopulations

Gnomad AFR

AF:

0.370

Gnomad AMI

AF:

0.533

Gnomad AMR

AF:

0.461

Gnomad ASJ

AF:

0.426

Gnomad EAS

AF:

0.321

Gnomad SAS

AF:

0.464

Gnomad FIN

AF:

0.537

Gnomad MID

AF:

0.459

Gnomad NFE

AF:

0.497

Gnomad OTH

AF:

0.458

GnomAD4 exome

AF:

0.478

AC:

76902

AN:

160898

Hom.:

18940

Cov.:

AF XY:

0.476

AC XY:

40849

AN XY:

85832

show subpopulations

African (AFR)

AF:

0.358

AC:

949

AN:

2650

American (AMR)

AF:

0.461

AC:

1749

AN:

3794

Ashkenazi Jewish (ASJ)

AF:

0.440

AC:

1917

AN:

4358

East Asian (EAS)

AF:

0.311

AC:

2068

AN:

6646

South Asian (SAS)

AF:

0.455

AC:

11048

AN:

24276

European-Finnish (FIN)

AF:

0.523

AC:

4759

AN:

9106

Middle Eastern (MID)

AF:

0.423

AC:

309

AN:

730

European-Non Finnish (NFE)

AF:

0.498

AC:

49843

AN:

100072

Other (OTH)

AF:

0.460

AC:

4260

AN:

9266

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1888

3775

5663

7550

9438

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

200

400

600

800

1000

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.452

AC:

68847

AN:

152158

Hom.:

15845

Cov.:

AF XY:

0.456

AC XY:

33899

AN XY:

74390

show subpopulations

African (AFR)

AF:

0.370

AC:

15353

AN:

41540

American (AMR)

AF:

0.461

AC:

7044

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.426

AC:

1479

AN:

3470

East Asian (EAS)

AF:

0.322

AC:

1649

AN:

5128

South Asian (SAS)

AF:

0.464

AC:

2239

AN:

4828

European-Finnish (FIN)

AF:

0.537

AC:

5694

AN:

10610

Middle Eastern (MID)

AF:

0.469

AC:

138

AN:

294

European-Non Finnish (NFE)

AF:

0.497

AC:

33795

AN:

67978

Other (OTH)

AF:

0.461

AC:

971

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1979

3958

5938

7917

9896

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

630

1260

1890

2520

3150

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.466

Hom.:

2139

Bravo

AF:

0.443

Asia WGS

AF:

0.378

AC:

1320

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

9.2

(source)

DANN

Benign

0.90

PhyloP100

1.1

PromoterAI

0.096

Neutral

(source)

Mutation Taster

=300/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over