rs4935752

Positions:

• chr11-120818410-A-C
• chr11-120818410-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014619.5(GRIK4):​c.346-1345A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 152,144 control chromosomes in the GnomAD database, including 7,412 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 0.29 (7412 hom., cov: 33)
• Consequence: GRIK4 NM_014619.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.650

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]

LOC105369532 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GRIK4	NM_014619.5	c.346-1345A>C		intron_variant		ENST00000527524.8	NP_055434.2
LOC105369532	NR_133008.1	n.155+551T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GRIK4	ENST00000527524.8	c.346-1345A>C		intron_variant		2	NM_014619.5	ENSP00000435648	P1
GRIK4	ENST00000438375.2	c.346-1345A>C		intron_variant		1		ENSP00000404063	P1
GRIK4	ENST00000533291.5	n.744-1345A>C		intron_variant, non_coding_transcript_variant		1
GRIK4	ENST00000638419.1	c.346-1345A>C		intron_variant		5		ENSP00000492086	P1

Frequencies

GnomAD3 genomes AF: 0.292 AC: 44400 AN: 152026 Hom.: 7420 Cov.: 33

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.292 AC: 44397 AN: 152144 Hom.: 7412 Cov.: 33 AF XY: 0.293 AC XY: 21813 AN XY: 74384

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.253

Gnomad4 ASJ AF: 0.382

Gnomad4 EAS AF: 0.425

Gnomad4 SAS AF: 0.316

Gnomad4 FIN AF: 0.414

Gnomad4 NFE AF: 0.365

Gnomad4 OTH AF: 0.314

Alfa AF: 0.349 Hom.: 12841

Bravo AF: 0.274

Asia WGS AF: 0.346 AC: 1201 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.0
DANN	Benign	0.60

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: rs4935752; hg19: chr11-120689119;