rs690533

Variant summary

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

The NM_000835.6(GRIN2C):​c.399+660C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.732 in 152,470 control chromosomes in the GnomAD database, including 41,111 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 0.73 ( 41016 hom., cov: 33)
Exomes 𝑓: 0.73 ( 95 hom. )

Consequence

GRIN2C
NM_000835.6 intron

Scores

1

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0850
Variant links:
Genes affected
GRIN2C (HGNC:4587): (glutamate ionotropic receptor NMDA type subunit 2C) This gene encodes a subunit of the N-methyl-D-aspartate (NMDA) receptor, which is a subtype of ionotropic glutamate receptor. NMDA receptors are found in the central nervous system, are permeable to cations and have an important role in physiological processes such as learning, memory, and synaptic development. The receptor is a tetramer of different subunits (typically heterodimer of subunit 1 with one or more of subunits 2A-D), forming a channel that is permeable to calcium, potassium, and sodium, and whose properties are determined by subunit composition. Alterations in the subunit composition of the receptor are associated with pathophysiological conditions such as Parkinson's disease, Alzheimer's disease, depression, and schizophrenia. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2013]

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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=-0.88).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.777 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
GRIN2CNM_000835.6 linkuse as main transcriptc.399+660C>T intron_variant ENST00000293190.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
GRIN2CENST00000293190.10 linkuse as main transcriptc.399+660C>T intron_variant 1 NM_000835.6 P1

Frequencies

GnomAD3 genomes
AF:
0.732
AC:
111288
AN:
152000
Hom.:
40982
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.709
Gnomad AMI
AF:
0.787
Gnomad AMR
AF:
0.788
Gnomad ASJ
AF:
0.626
Gnomad EAS
AF:
0.587
Gnomad SAS
AF:
0.735
Gnomad FIN
AF:
0.751
Gnomad MID
AF:
0.703
Gnomad NFE
AF:
0.747
Gnomad OTH
AF:
0.725
GnomAD4 exome
AF:
0.727
AC:
256
AN:
352
Hom.:
95
Cov.:
0
AF XY:
0.728
AC XY:
166
AN XY:
228
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
1.00
Gnomad4 EAS exome
AF:
0.625
Gnomad4 SAS exome
AF:
0.500
Gnomad4 FIN exome
AF:
0.726
Gnomad4 NFE exome
AF:
0.739
Gnomad4 OTH exome
AF:
0.767
GnomAD4 genome
AF:
0.732
AC:
111374
AN:
152118
Hom.:
41016
Cov.:
33
AF XY:
0.735
AC XY:
54639
AN XY:
74356
show subpopulations
Gnomad4 AFR
AF:
0.709
Gnomad4 AMR
AF:
0.788
Gnomad4 ASJ
AF:
0.626
Gnomad4 EAS
AF:
0.587
Gnomad4 SAS
AF:
0.735
Gnomad4 FIN
AF:
0.751
Gnomad4 NFE
AF:
0.747
Gnomad4 OTH
AF:
0.726
Alfa
AF:
0.742
Hom.:
6731
Bravo
AF:
0.730

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
2.3
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

Splicing

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: rs690533; hg19: chr17-72850173; API