rs34360565
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Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_021956.5(GRIK2):āc.939T>Cā(p.Asp313=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00512 in 1,612,992 control chromosomes in the GnomAD database, including 48 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.0096 ( 13 hom., cov: 32)
Exomes š: 0.0046 ( 35 hom. )
Consequence
GRIK2
NM_021956.5 synonymous
NM_021956.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.96
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 -19 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.43).
BP6
?
Variant 6-101686341-T-C is Benign according to our data. Variant chr6-101686341-T-C is described in ClinVar as [Benign]. Clinvar id is 129177.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=1.96 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00965 (1469/152232) while in subpopulation AFR AF= 0.0247 (1028/41550). AF 95% confidence interval is 0.0235. There are 13 homozygotes in gnomad4. There are 692 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 13 AD,AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GRIK2 | NM_021956.5 | c.939T>C | p.Asp313= | synonymous_variant | 7/17 | ENST00000369134.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GRIK2 | ENST00000369134.9 | c.939T>C | p.Asp313= | synonymous_variant | 7/17 | 5 | NM_021956.5 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00965 AC: 1468AN: 152114Hom.: 13 Cov.: 32
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GnomAD3 exomes AF: 0.00446 AC: 1119AN: 251010Hom.: 8 AF XY: 0.00410 AC XY: 556AN XY: 135662
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GnomAD4 exome AF: 0.00465 AC: 6789AN: 1460760Hom.: 35 Cov.: 30 AF XY: 0.00451 AC XY: 3278AN XY: 726744
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GnomAD4 genome ? AF: 0.00965 AC: 1469AN: 152232Hom.: 13 Cov.: 32 AF XY: 0.00930 AC XY: 692AN XY: 74434
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jul 08, 2013 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
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Name
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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