rs1954787

chr11-120792654-T-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_014619.5(GRIK4):c.83-10039T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.458 in 151,946 control chromosomes in the GnomAD database, including 18,642 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.46 (18642 hom., cov: 32)
• Consequence: GRIK4 NM_014619.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.30

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BP6: Variant 11-120792654-T-C is Benign according to our data. Variant chr11-120792654-T-C is described in ClinVar as [Benign]. Clinvar id is 225967.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.824 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GRIK4	NM_014619.5	c.83-10039T>C		intron_variant		ENST00000527524.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GRIK4	ENST00000527524.8	c.83-10039T>C		intron_variant		2	NM_014619.5	P1

Frequencies

GnomAD3 genomes AF: 0.458 AC: 69554 AN: 151828 Hom.: 18635 Cov.: 32

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.845

Gnomad SAS AF: 0.574

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.489

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.458 AC: 69573 AN: 151946 Hom.: 18642 Cov.: 32 AF XY: 0.459 AC XY: 34060 AN XY: 74240

Gnomad4 AFR AF: 0.175

Gnomad4 AMR AF: 0.596

Gnomad4 ASJ AF: 0.546

Gnomad4 EAS AF: 0.845

Gnomad4 SAS AF: 0.574

Gnomad4 FIN AF: 0.488

Gnomad4 NFE AF: 0.551

Gnomad4 OTH AF: 0.492

Alfa AF: 0.542 Hom.: 46888

Bravo AF: 0.457

Asia WGS AF: 0.678 AC: 2355 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Mar 09, 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. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.63
Dann	Benign	0.73

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1954787; hg19: chr11-120663363;