chr11-120912660-A-G

Variant names:

• chr11-120912660-A-G
• rs17124538
• NM_014619.5:c.1476+7167A>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.1476+7167A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.074 in 152,276 control chromosomes in the GnomAD database, including 517 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 0.074 (517 hom., cov: 31)
• Consequence: GRIK4 NM_014619.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0490
• 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]

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 (AFR) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GRIK4	NM_014619.5	c.1476+7167A>G		intron_variant	Intron 13 of 20	ENST00000527524.8	NP_055434.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GRIK4	ENST00000527524.8	c.1476+7167A>G		intron_variant	Intron 13 of 20	2	NM_014619.5	ENSP00000435648.2
GRIK4	ENST00000438375.2	c.1476+7167A>G		intron_variant	Intron 12 of 19	1		ENSP00000404063.2
GRIK4	ENST00000533291.5	n.1874+7167A>G		intron_variant	Intron 13 of 17	1
GRIK4	ENST00000638419.1	c.1476+7167A>G		intron_variant	Intron 13 of 20	5		ENSP00000492086.1

Frequencies

GnomAD3 genomes AF: 0.0740 AC: 11256 AN: 152158 Hom.: 515 Cov.: 31

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.0530

Gnomad ASJ AF: 0.0418

Gnomad EAS AF: 0.0735

Gnomad SAS AF: 0.0936

Gnomad FIN AF: 0.0589

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0480

Gnomad OTH AF: 0.0603

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

GnomAD4 genome AF: 0.0740 AC: 11261 AN: 152276 Hom.: 517 Cov.: 31 AF XY: 0.0754 AC XY: 5614 AN XY: 74466

African (AFR) AF: 0.130 AC: 5411 AN: 41528

American (AMR) AF: 0.0528 AC: 808 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0418 AC: 145 AN: 3470

East Asian (EAS) AF: 0.0731 AC: 379 AN: 5186

South Asian (SAS) AF: 0.0941 AC: 454 AN: 4826

European-Finnish (FIN) AF: 0.0589 AC: 626 AN: 10622

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0480 AC: 3268 AN: 68028

Other (OTH) AF: 0.0597 AC: 126 AN: 2112

Alfa AF: 0.0548 Hom.: 446

Bravo AF: 0.0768

Asia WGS AF: 0.0770 AC: 267 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	2.1
DANN	Benign	0.44
PhyloP100		-0.049
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: rs17124538; hg19: chr11-120783369;