rs10790400

Variant names:

• chr11-120686382-A-T
• rs10790400
• NM_014619.5:c.82+25982A>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+25982A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.492 in 152,070 control chromosomes in the GnomAD database, including 18,636 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 0.49 (18636 hom., cov: 33)
• Consequence: GRIK4 NM_014619.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.62
• Publications: 5 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.551 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GRIK4	NM_014619.5	c.82+25982A>T		intron_variant	Intron 3 of 20	ENST00000527524.8	NP_055434.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GRIK4	ENST00000527524.8	c.82+25982A>T		intron_variant	Intron 3 of 20	2	NM_014619.5	ENSP00000435648.2

Frequencies

GnomAD3 genomes AF: 0.492 AC: 74695 AN: 151952 Hom.: 18602 Cov.: 33

Gnomad AFR AF: 0.556

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.513

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.478

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.473

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

GnomAD4 genome AF: 0.492 AC: 74775 AN: 152070 Hom.: 18636 Cov.: 33 AF XY: 0.491 AC XY: 36526 AN XY: 74316

African (AFR) AF: 0.557 AC: 23087 AN: 41482

American (AMR) AF: 0.465 AC: 7094 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.513 AC: 1780 AN: 3468

East Asian (EAS) AF: 0.497 AC: 2573 AN: 5174

South Asian (SAS) AF: 0.474 AC: 2283 AN: 4816

European-Finnish (FIN) AF: 0.478 AC: 5051 AN: 10570

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.460 AC: 31288 AN: 67980

Other (OTH) AF: 0.475 AC: 1000 AN: 2106

Alfa AF: 0.471 Hom.: 2142

Bravo AF: 0.493

Asia WGS AF: 0.467 AC: 1624 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	8.0
DANN	Benign	0.37
PhyloP100		1.6
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: rs10790400; hg19: chr11-120557091;