rs3213607
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1
The NM_021956.5(GRIK2):c.2226C>A(p.Ile742=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0655 in 1,608,300 control chromosomes in the GnomAD database, including 3,612 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Genomes: 𝑓 0.068 ( 351 hom., cov: 31)
Exomes 𝑓: 0.065 ( 3261 hom. )
Consequence
GRIK2
NM_021956.5 synonymous
NM_021956.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.309
Genes affected
GRIK2 (HGNC:4580): (glutamate ionotropic receptor kainate type subunit 2) Glutamate receptors are the predominant excitatory neurotransmitter receptors in the mammalian brain and are activated in a variety of normal neurophysiologic processes. This gene product belongs to the kainate family of glutamate receptors, which are composed of four subunits and function as ligand-activated ion channels. The subunit encoded by this gene is subject to RNA editing at multiple sites within the first and second transmembrane domains, which is thought to alter the structure and function of the receptor complex. Alternatively spliced transcript variants encoding different isoforms have also been described for this gene. Mutations in this gene have been associated with autosomal recessive cognitive disability. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.51).
BP6
Variant 6-102035481-C-A is Benign according to our data. Variant chr6-102035481-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 129172.Status of the report is no_assertion_criteria_provided, 0 stars.
BP7
Synonymous conserved (PhyloP=-0.309 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.079 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GRIK2 | NM_021956.5 | c.2226C>A | p.Ile742= | synonymous_variant | 15/17 | ENST00000369134.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GRIK2 | ENST00000369134.9 | c.2226C>A | p.Ile742= | synonymous_variant | 15/17 | 5 | NM_021956.5 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0684 AC: 10328AN: 151102Hom.: 350 Cov.: 31
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GnomAD3 exomes AF: 0.0649 AC: 16261AN: 250652Hom.: 591 AF XY: 0.0642 AC XY: 8698AN XY: 135478
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GnomAD4 exome AF: 0.0652 AC: 95072AN: 1457080Hom.: 3261 Cov.: 29 AF XY: 0.0650 AC XY: 47097AN XY: 725072
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GnomAD4 genome AF: 0.0683 AC: 10334AN: 151220Hom.: 351 Cov.: 31 AF XY: 0.0685 AC XY: 5060AN XY: 73852
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, no assertion criteria provided | clinical testing | Genetic Services Laboratory, University of Chicago | - | Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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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