11-120919143-T-C

Variant names:

• chr11-120919143-T-C
• rs949295
• NM_014619.5:c.1476+13650T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014619.5(GRIK4):​c.1476+13650T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.57 in 152,064 control chromosomes in the GnomAD database, including 26,259 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 0.57 (26259 hom., cov: 32)
• Consequence: GRIK4 NM_014619.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.470
• Publications: 6 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.779 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.1476+13650T>C		intron	N/A	NP_055434.2
	GRIK4	NM_001282470.3		c.1476+13650T>C		intron	N/A	NP_001269399.1	A0A8D9PH79
	GRIK4	NM_001440402.1		c.1476+13650T>C		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.1476+13650T>C		intron	N/A	ENSP00000435648.2	Q16099
	GRIK4	ENST00000438375.2	TSL:1	c.1476+13650T>C		intron	N/A	ENSP00000404063.2	Q16099
	GRIK4	ENST00000533291.5	TSL:1	n.1874+13650T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.570 AC: 86597 AN: 151946 Hom.: 26217 Cov.: 32

Gnomad AFR AF: 0.786

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.527

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.540

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.552

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

GnomAD4 genome AF: 0.570 AC: 86703 AN: 152064 Hom.: 26259 Cov.: 32 AF XY: 0.567 AC XY: 42108 AN XY: 74320

African (AFR) AF: 0.786 AC: 32622 AN: 41514

American (AMR) AF: 0.526 AC: 8038 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.405 AC: 1403 AN: 3464

East Asian (EAS) AF: 0.540 AC: 2783 AN: 5158

South Asian (SAS) AF: 0.314 AC: 1509 AN: 4812

European-Finnish (FIN) AF: 0.547 AC: 5772 AN: 10550

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.482 AC: 32755 AN: 67974

Other (OTH) AF: 0.550 AC: 1158 AN: 2106

Alfa AF: 0.505 Hom.: 62083

Bravo AF: 0.581

Asia WGS AF: 0.454 AC: 1580 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.2
DANN	Benign	0.71
PhyloP100		-0.47
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: rs949295; hg19: chr11-120789852;