rs2154490

Variant names:

• chr21-29543641-A-G
• rs2154490
• NM_001330994.2:c.2608-5757T>C

Variant summary

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

The NM_001330994.2(GRIK1):​c.2608-5757T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.755 in 152,014 control chromosomes in the GnomAD database, including 43,442 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 0.75 (43442 hom., cov: 31)
• Consequence: GRIK1 NM_001330994.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.42
• Publications: 10 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]

BACH1 (HGNC:935): (BTB domain and CNC homolog 1) This gene encodes a transcription factor that belongs to the cap'n'collar type of basic region leucine zipper factor family (CNC-bZip). The encoded protein contains broad complex, tramtrack, bric-a-brac/poxvirus and zinc finger (BTB/POZ) domains, which is atypical of CNC-bZip family members. These BTB/POZ domains facilitate protein-protein interactions and formation of homo- and/or hetero-oligomers. When this encoded protein forms a heterodimer with MafK, it functions as a repressor of Maf recognition element (MARE) and transcription is repressed. Multiple alternatively spliced transcript variants have been identified for this gene. [provided by RefSeq, May 2009]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.821 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.2608-5757T>C		intron	N/A	NP_001317923.1
	GRIK1	NM_001330993.2		c.2563-5757T>C		intron	N/A	NP_001317922.1
	GRIK1	NM_001320616.2		c.2608-6256T>C		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.2608-5757T>C		intron	N/A	ENSP00000327687.4
	GRIK1	ENST00000389125.7	TSL:1	c.2563-6256T>C		intron	N/A	ENSP00000373777.3
	GRIK1	ENST00000399914.5	TSL:5	c.2563-5757T>C		intron	N/A	ENSP00000382798.1

Frequencies

GnomAD3 genomes AF: 0.755 AC: 114650 AN: 151896 Hom.: 43394 Cov.: 31

Gnomad AFR AF: 0.741

Gnomad AMI AF: 0.826

Gnomad AMR AF: 0.825

Gnomad ASJ AF: 0.754

Gnomad EAS AF: 0.843

Gnomad SAS AF: 0.781

Gnomad FIN AF: 0.716

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.744

Gnomad OTH AF: 0.749

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

GnomAD4 genome AF: 0.755 AC: 114751 AN: 152014 Hom.: 43442 Cov.: 31 AF XY: 0.757 AC XY: 56248 AN XY: 74290

African (AFR) AF: 0.741 AC: 30717 AN: 41456

American (AMR) AF: 0.825 AC: 12600 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.754 AC: 2617 AN: 3472

East Asian (EAS) AF: 0.842 AC: 4355 AN: 5170

South Asian (SAS) AF: 0.783 AC: 3762 AN: 4804

European-Finnish (FIN) AF: 0.716 AC: 7560 AN: 10552

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.744 AC: 50569 AN: 67970

Other (OTH) AF: 0.749 AC: 1584 AN: 2116

Alfa AF: 0.742 Hom.: 7366

Bravo AF: 0.762

Asia WGS AF: 0.774 AC: 2690 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.0060
DANN	Benign	0.51
PhyloP100		-3.4
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: rs2154490; hg19: chr21-30915962;