rs690533
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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
NM_000835.6 intron
Scores
1
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0850
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 |
---|---|---|---|---|---|---|---|
GRIN2C | NM_000835.6 | c.399+660C>T | intron_variant | ENST00000293190.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GRIN2C | ENST00000293190.10 | c.399+660C>T | intron_variant | 1 | NM_000835.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.732 AC: 111288AN: 152000Hom.: 40982 Cov.: 33
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GnomAD4 exome AF: 0.727 AC: 256AN: 352Hom.: 95 Cov.: 0 AF XY: 0.728 AC XY: 166AN XY: 228
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GnomAD4 genome AF: 0.732 AC: 111374AN: 152118Hom.: 41016 Cov.: 33 AF XY: 0.735 AC XY: 54639AN XY: 74356
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ClinVar
Not reported inComputational scores
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Prediction
BayesDel_noAF
Benign
CADD
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at