21-29660643-G-A

Variant names:

• chr21-29660643-G-A
• rs363568
• NM_001330994.2:c.727-5780C>T

Variant summary

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

The NM_001330994.2(GRIK1):​c.727-5780C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0714 in 152,142 control chromosomes in the GnomAD database, including 536 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 0.071 (536 hom., cov: 32)
• Consequence: GRIK1 NM_001330994.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.703
• Publications: 1 publications found

Genes affected

GRIK1 (HGNC:4579): (glutamate ionotropic receptor kainate type subunit 1) 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. The subunit encoded by this gene is subject to RNA editing (CAG->CGG; Q->R) within the second transmembrane domain, which is thought to alter the properties of ion flow. Alternative splicing, resulting in transcript variants encoding different isoforms, has been noted for this gene. [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=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0989 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001330994.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GRIK1	NM_001330994.2	MANE Select	c.727-5780C>T		intron	N/A	NP_001317923.1
	GRIK1	NM_001330993.2		c.727-5780C>T		intron	N/A	NP_001317922.1
	GRIK1	NM_001320616.2		c.727-5780C>T		intron	N/A	NP_001307545.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GRIK1	ENST00000327783.9	TSL:5 MANE Select	c.727-5780C>T		intron	N/A	ENSP00000327687.4
	GRIK1	ENST00000399907.6	TSL:1	c.727-5780C>T		intron	N/A	ENSP00000382791.1
	GRIK1	ENST00000389125.7	TSL:1	c.727-5780C>T		intron	N/A	ENSP00000373777.3

Frequencies

GnomAD3 genomes AF: 0.0714 AC: 10862 AN: 152024 Hom.: 536 Cov.: 32

Gnomad AFR AF: 0.0188

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0733

Gnomad ASJ AF: 0.0963

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0361

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.0856

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

GnomAD4 genome AF: 0.0714 AC: 10860 AN: 152142 Hom.: 536 Cov.: 32 AF XY: 0.0725 AC XY: 5392 AN XY: 74368

African (AFR) AF: 0.0187 AC: 776 AN: 41500

American (AMR) AF: 0.0732 AC: 1119 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0963 AC: 334 AN: 3468

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5180

South Asian (SAS) AF: 0.0364 AC: 175 AN: 4814

European-Finnish (FIN) AF: 0.132 AC: 1393 AN: 10568

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6863 AN: 68000

Other (OTH) AF: 0.0843 AC: 178 AN: 2112

Alfa AF: 0.0912 Hom.: 363

Bravo AF: 0.0649

Asia WGS AF: 0.0180 AC: 63 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	10
DANN	Benign	0.77
PhyloP100		0.70
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: rs363568; hg19: chr21-31032963;