11-120967112-G-A
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_014619.5(GRIK4):c.2267-83G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.571 in 1,463,536 control chromosomes in the GnomAD database, including 243,071 homozygotes. 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: 𝑓 0.54 ( 22852 hom., cov: 32)
Exomes 𝑓: 0.57 ( 220219 hom. )
Consequence
GRIK4
NM_014619.5 intron
NM_014619.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.55
Genes affected
GRIK4 (HGNC:4582): (glutamate ionotropic receptor kainate type subunit 4) This gene encodes a protein that belongs to the glutamate-gated ionic channel family. Glutamate functions as the major excitatory neurotransmitter in the central nervous system through activation of ligand-gated ion channels and G protein-coupled membrane receptors. The protein encoded by this gene forms functional heteromeric kainate-preferring ionic channels with the subunits encoded by related gene family members. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.588 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GRIK4 | NM_014619.5 | c.2267-83G>A | intron_variant | ENST00000527524.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GRIK4 | ENST00000527524.8 | c.2267-83G>A | intron_variant | 2 | NM_014619.5 | P1 | |||
GRIK4 | ENST00000438375.2 | c.2267-83G>A | intron_variant | 1 | P1 | ||||
GRIK4 | ENST00000638419.1 | c.2267-83G>A | intron_variant | 5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.542 AC: 82350AN: 151990Hom.: 22842 Cov.: 32
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GnomAD4 exome AF: 0.575 AC: 753843AN: 1311428Hom.: 220219 AF XY: 0.571 AC XY: 369739AN XY: 647278
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GnomAD4 genome AF: 0.542 AC: 82389AN: 152108Hom.: 22852 Cov.: 32 AF XY: 0.540 AC XY: 40163AN XY: 74364
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at