rs10502240

Variant names:

• chr11-120677203-C-T
• rs10502240
• NM_014619.5:c.82+16803C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014619.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GRIK4	NM_014619.5	MANE Select	c.82+16803C>T		intron	N/A	NP_055434.2
	GRIK4	NM_001282470.3		c.82+16803C>T		intron	N/A	NP_001269399.1
	GRIK4	NM_001440402.1		c.82+16803C>T		intron	N/A	NP_001427331.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GRIK4	ENST00000527524.8	TSL:2 MANE Select	c.82+16803C>T		intron	N/A	ENSP00000435648.2
	GRIK4	ENST00000438375.2	TSL:1	c.82+16803C>T		intron	N/A	ENSP00000404063.2
	GRIK4	ENST00000533291.5	TSL:1	n.480+16803C>T		intron	N/A

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

African (AFR) AF: 0.199 AC: 8245 AN: 41506

American (AMR) AF: 0.117 AC: 1794 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.137 AC: 476 AN: 3470

East Asian (EAS) AF: 0.0193 AC: 100 AN: 5178

South Asian (SAS) AF: 0.232 AC: 1113 AN: 4802

European-Finnish (FIN) AF: 0.117 AC: 1239 AN: 10584

Middle Eastern (MID) AF: 0.140 AC: 41 AN: 292

European-Non Finnish (NFE) AF: 0.150 AC: 10215 AN: 68002

Other (OTH) AF: 0.153 AC: 324 AN: 2112

Alfa AF: 0.150 Hom.: 3235

Bravo AF: 0.157

Asia WGS AF: 0.134 AC: 464 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	11
DANN	Benign	0.69
PhyloP100		-0.35
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10502240; hg19: chr11-120547912;