GeneBe

rs2301364

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_007327.4(GRIN1):​c.258+339T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)

Consequence

GRIN1
NM_007327.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.277

Publications

7 publications found
Variant links:
Genes affected
GRIN1 (HGNC:4584): (glutamate ionotropic receptor NMDA type subunit 1) The protein encoded by this gene is a critical subunit of N-methyl-D-aspartate receptors, members of the glutamate receptor channel superfamily which are heteromeric protein complexes with multiple subunits arranged to form a ligand-gated ion channel. These subunits play a key role in the plasticity of synapses, which is believed to underlie memory and learning. Cell-specific factors are thought to control expression of different isoforms, possibly contributing to the functional diversity of the subunits. Alternatively spliced transcript variants have been described. [provided by RefSeq, Jul 2008]
GRIN1 Gene-Disease associations (from GenCC):
  • neurodevelopmental disorder with or without hyperkinetic movements and seizures, autosomal dominant
    Inheritance: AD Classification: DEFINITIVE, STRONG, MODERATE Submitted by: G2P, Labcorp Genetics (formerly Invitae), Ambry Genetics
  • complex neurodevelopmental disorder
    Inheritance: AR, AD Classification: DEFINITIVE Submitted by: ClinGen
  • neurodevelopmental disorder with or without hyperkinetic movements and seizures, autosomal recessive
    Inheritance: AR Classification: DEFINITIVE, MODERATE Submitted by: Ambry Genetics, G2P
  • developmental and epileptic encephalopathy 101
    Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
  • autosomal dominant non-syndromic intellectual disability
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007327.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
GRIN1
NM_007327.4
MANE Select
c.258+339T>A
intron
N/ANP_015566.1Q05586-1
GRIN1
NM_001437330.1
c.258+339T>A
intron
N/ANP_001424259.1
GRIN1
NM_001185090.2
c.258+339T>A
intron
N/ANP_001172019.1Q05586-6

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
GRIN1
ENST00000371561.8
TSL:1 MANE Select
c.258+339T>A
intron
N/AENSP00000360616.3Q05586-1
GRIN1
ENST00000371553.8
TSL:1
c.258+339T>A
intron
N/AENSP00000360608.3Q05586-6
GRIN1
ENST00000371560.5
TSL:1
c.258+339T>A
intron
N/AENSP00000360615.3Q05586-7

Frequencies

GnomAD3 genomes
Cov.:
33
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
1.5
DANN
Benign
0.86
PhyloP100
-0.28

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

Other links and lift over

dbSNP: rs2301364; hg19: chr9-140034535; API