rs10502240

chr11-120677203-C-T

Variant summary

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

The NM_014619.5(GRIK4):c.82+16803C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 152,148 control chromosomes in the GnomAD database, including 2,010 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 0.16 (2010 hom., cov: 32)
• Consequence: GRIK4 NM_014619.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.352

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GRIK4	NM_014619.5	c.82+16803C>T		intron_variant		ENST00000527524.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GRIK4	ENST00000527524.8	c.82+16803C>T		intron_variant		2	NM_014619.5	P1

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23663 AN: 152030 Hom.: 2005 Cov.: 32

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.172

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.0193

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.140

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.156 AC: 23703 AN: 152148 Hom.: 2010 Cov.: 32 AF XY: 0.154 AC XY: 11456 AN XY: 74364

Gnomad4 AFR AF: 0.199

Gnomad4 AMR AF: 0.117

Gnomad4 ASJ AF: 0.137

Gnomad4 EAS AF: 0.0193

Gnomad4 SAS AF: 0.232

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.153

Alfa AF: 0.149 Hom.: 2562

Bravo AF: 0.157

Asia WGS AF: 0.134 AC: 464 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	11
Dann	Benign	0.69

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: rs10502240; hg19: chr11-120547912;