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GeneBe

rs2485528

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_133445.3(GRIN3A):c.700-19785A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 152,038 control chromosomes in the GnomAD database, including 13,256 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 0.41 ( 13256 hom., cov: 32)

Consequence

GRIN3A
NM_133445.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.38
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.462 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
GRIN3ANM_133445.3 linkuse as main transcriptc.700-19785A>G intron_variant ENST00000361820.6
GRIN3AXM_011518211.3 linkuse as main transcriptc.700-19785A>G intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
GRIN3AENST00000361820.6 linkuse as main transcriptc.700-19785A>G intron_variant 1 NM_133445.3 P1

Frequencies

GnomAD3 genomes
AF:
0.411
AC:
62500
AN:
151920
Hom.:
13248
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.301
Gnomad AMI
AF:
0.364
Gnomad AMR
AF:
0.429
Gnomad ASJ
AF:
0.431
Gnomad EAS
AF:
0.339
Gnomad SAS
AF:
0.472
Gnomad FIN
AF:
0.466
Gnomad MID
AF:
0.401
Gnomad NFE
AF:
0.467
Gnomad OTH
AF:
0.417
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.411
AC:
62524
AN:
152038
Hom.:
13256
Cov.:
32
AF XY:
0.414
AC XY:
30749
AN XY:
74302
show subpopulations
Gnomad4 AFR
AF:
0.301
Gnomad4 AMR
AF:
0.429
Gnomad4 ASJ
AF:
0.431
Gnomad4 EAS
AF:
0.339
Gnomad4 SAS
AF:
0.472
Gnomad4 FIN
AF:
0.466
Gnomad4 NFE
AF:
0.467
Gnomad4 OTH
AF:
0.417
Alfa
AF:
0.436
Hom.:
1792
Bravo
AF:
0.403
Asia WGS
AF:
0.366
AC:
1273
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
Cadd
Benign
16
Dann
Benign
0.63

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.

Other links and lift over

dbSNP: rs2485528; hg19: chr9-104469267; COSMIC: COSV62457651; API