chr17-74846088-C-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_000835.6(GRIN2C):c.2328G>A(p.Ala776=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00374 in 1,614,144 control chromosomes in the GnomAD database, including 18 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0024 ( 2 hom., cov: 32)
Exomes 𝑓: 0.0039 ( 16 hom. )
Consequence
GRIN2C
NM_000835.6 synonymous
NM_000835.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.58
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 -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.65).
BP6
?
Variant 17-74846088-C-T is Benign according to our data. Variant chr17-74846088-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2648236.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-3.58 with no splicing effect.
BS2
?
High Homozygotes in GnomAd at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GRIN2C | NM_000835.6 | c.2328G>A | p.Ala776= | synonymous_variant | 11/13 | ENST00000293190.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GRIN2C | ENST00000293190.10 | c.2328G>A | p.Ala776= | synonymous_variant | 11/13 | 1 | NM_000835.6 | P1 | |
GRIN2C | ENST00000347612.4 | c.2328G>A | p.Ala776= | synonymous_variant | 11/12 | 1 | |||
GRIN2C | ENST00000584176.1 | n.6071G>A | non_coding_transcript_exon_variant | 7/9 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00240 AC: 366AN: 152240Hom.: 2 Cov.: 32
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GnomAD3 exomes AF: 0.00265 AC: 666AN: 251266Hom.: 2 AF XY: 0.00253 AC XY: 343AN XY: 135806
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GnomAD4 exome AF: 0.00388 AC: 5667AN: 1461786Hom.: 16 Cov.: 32 AF XY: 0.00385 AC XY: 2800AN XY: 727206
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2023 | GRIN2C: BP4, BP7, BS2 - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at