chr11-120614101-A-G

Variant names:

• chr11-120614101-A-G
• rs1317814
• NM_014619.5:c.-158-39584A>G

Variant summary

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

The NM_014619.5(GRIK4):​c.-158-39584A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.298 in 152,050 control chromosomes in the GnomAD database, including 7,279 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 0.30 (7279 hom., cov: 32)
• Consequence: GRIK4 NM_014619.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 3 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]

ENSG00000297990 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.331 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.-158-39584A>G		intron	N/A	NP_055434.2
	GRIK4	NM_001282470.3		c.-50-46168A>G		intron	N/A	NP_001269399.1	A0A8D9PH79
	GRIK4	NM_001440402.1		c.-159+37538A>G		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.-158-39584A>G		intron	N/A	ENSP00000435648.2	Q16099
	GRIK4	ENST00000438375.2	TSL:1	c.-50-46168A>G		intron	N/A	ENSP00000404063.2	Q16099
	GRIK4	ENST00000533291.5	TSL:1	n.241-39584A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.298 AC: 45285 AN: 151934 Hom.: 7277 Cov.: 32

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.00270

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.298 AC: 45322 AN: 152050 Hom.: 7279 Cov.: 32 AF XY: 0.294 AC XY: 21822 AN XY: 74306

African (AFR) AF: 0.302 AC: 12519 AN: 41458

American (AMR) AF: 0.201 AC: 3073 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.297 AC: 1030 AN: 3468

East Asian (EAS) AF: 0.00271 AC: 14 AN: 5170

South Asian (SAS) AF: 0.154 AC: 742 AN: 4814

European-Finnish (FIN) AF: 0.413 AC: 4363 AN: 10562

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.335 AC: 22742 AN: 67976

Other (OTH) AF: 0.284 AC: 600 AN: 2114

Alfa AF: 0.314 Hom.: 967

Bravo AF: 0.285

Asia WGS AF: 0.107 AC: 373 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.25
DANN	Benign	0.22
PhyloP100		-1.3
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: rs1317814; hg19: chr11-120484810;