9-137139487-A-G
Variant names:
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 3P and 2B. PVS1_SupportingPM2BP6_Moderate
The NM_007327.4(GRIN1):c.1A>G(p.Met1?) variant causes a start lost change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 32)
Consequence
GRIN1
NM_007327.4 start_lost
NM_007327.4 start_lost
Scores
3
4
9
Clinical Significance
Conservation
PhyloP100: 2.66
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]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PVS1
Start lost variant, no pathogenic variants between lost start and next in-frame start position. Next in-frame start position is after 4 codons. Genomic position: 137139496. Lost 0.004 part of the original CDS.
PM2
Very rare variant in population databases, with high coverage;
BP6
Variant 9-137139487-A-G is Benign according to our data. Variant chr9-137139487-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 3652142.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Cov.: 32
GnomAD4 exome
Cov.:
32
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Intellectual disability, autosomal dominant 8 Benign:1
May 07, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T;.;.;T;.;.;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Uncertain
D;D;D;D;D;D;D
M_CAP
Pathogenic
D
MetaRNN
Pathogenic
D;D;D;D;D;D;D
MetaSVM
Benign
T
PROVEAN
Benign
N;N;N;N;N;N;N
REVEL
Uncertain
Sift
Pathogenic
D;D;D;D;D;D;D
Sift4G
Benign
T;T;T;T;T;T;T
Polyphen
B;B;.;.;.;B;.
Vest4
MutPred
Loss of phosphorylation at S2 (P = 0.1027);Loss of phosphorylation at S2 (P = 0.1027);Loss of phosphorylation at S2 (P = 0.1027);Loss of phosphorylation at S2 (P = 0.1027);Loss of phosphorylation at S2 (P = 0.1027);Loss of phosphorylation at S2 (P = 0.1027);Loss of phosphorylation at S2 (P = 0.1027);
MVP
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.