rs201316377
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Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 1P and 8B. PP3BP6_Very_Strong
The NM_007327.4(GRIN1):c.2333+9C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000267 in 1,612,996 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.000053 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000024 ( 0 hom. )
Consequence
GRIN1
NM_007327.4 intron
NM_007327.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.116
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 Benign. Variant got -7 ACMG points.
PP3
?
Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
BP6
?
Variant 9-137163339-C-A is Benign according to our data. Variant chr9-137163339-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 240833.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GRIN1 | NM_007327.4 | c.2333+9C>A | intron_variant | ENST00000371561.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GRIN1 | ENST00000371561.8 | c.2333+9C>A | intron_variant | 1 | NM_007327.4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152198Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.00000400 AC: 1AN: 250234Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135612
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GnomAD4 exome AF: 0.0000240 AC: 35AN: 1460798Hom.: 0 Cov.: 34 AF XY: 0.0000220 AC XY: 16AN XY: 726702
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GnomAD4 genome ? AF: 0.0000526 AC: 8AN: 152198Hom.: 0 Cov.: 33 AF XY: 0.0000673 AC XY: 5AN XY: 74348
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 12, 2018 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Intellectual disability, autosomal dominant 8 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 05, 2023 | - - |
Computational scores
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BayesDel_noAF
Benign
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SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_DG_spliceai
Position offset: -3
Find out detailed SpliceAI scores and Pangolin per-transcript scores at