chr1-36937966-C-T

Variant names:

• chr1-36937966-C-T
• rs1160751
• NM_000831.4:c.116-46870G>A

Variant summary

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

The NM_000831.4(GRIK3):​c.116-46870G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.6 in 152,094 control chromosomes in the GnomAD database, including 29,196 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 0.60 (29196 hom., cov: 33)
• Consequence: GRIK3 NM_000831.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0810
• Publications: 3 publications found

Genes affected

GRIK3 (HGNC:4581): (glutamate ionotropic receptor kainate type subunit 3) Glutamate receptors are the predominant excitatory neurotransmitter receptors in the mammalian brain and are activated in a variety of normal neurophysiologic processes. This gene product belongs to the kainate family of glutamate receptors, which are composed of four subunits and function as ligand-activated ion channels. It is not certain if the subunit encoded by this gene is subject to RNA editing as the other 2 family members (GRIK1 and GRIK2). A Ser310Ala polymorphism has been associated with schizophrenia, and there are conflicting reports of its association with the pathogenesis of delirium tremens in alcoholics. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.822 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000831.4. 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
	GRIK3	NM_000831.4	MANE Select	c.116-46870G>A		intron	N/A	NP_000822.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GRIK3	ENST00000373091.8	TSL:1 MANE Select	c.116-46870G>A		intron	N/A	ENSP00000362183.3	Q13003-1
	GRIK3	ENST00000373093.4	TSL:1	c.116-46870G>A		intron	N/A	ENSP00000362185.4	Q13003-2

Frequencies

GnomAD3 genomes AF: 0.600 AC: 91170 AN: 151976 Hom.: 29176 Cov.: 33

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.705

Gnomad AMR AF: 0.711

Gnomad ASJ AF: 0.588

Gnomad EAS AF: 0.842

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.780

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.617

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

GnomAD4 genome AF: 0.600 AC: 91205 AN: 152094 Hom.: 29196 Cov.: 33 AF XY: 0.610 AC XY: 45316 AN XY: 74340

African (AFR) AF: 0.362 AC: 14991 AN: 41466

American (AMR) AF: 0.711 AC: 10873 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.588 AC: 2042 AN: 3470

East Asian (EAS) AF: 0.843 AC: 4361 AN: 5176

South Asian (SAS) AF: 0.677 AC: 3258 AN: 4810

European-Finnish (FIN) AF: 0.780 AC: 8257 AN: 10592

Middle Eastern (MID) AF: 0.575 AC: 168 AN: 292

European-Non Finnish (NFE) AF: 0.667 AC: 45309 AN: 67980

Other (OTH) AF: 0.618 AC: 1303 AN: 2108

Alfa AF: 0.634 Hom.: 36887

Bravo AF: 0.582

Asia WGS AF: 0.704 AC: 2447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
DANN	Benign	0.42
PhyloP100		0.081
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: rs1160751; hg19: chr1-37403567;