NM_001330994.2:c.1099-13018G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001330994.2(GRIK1):​c.1099-13018G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.547 in 152,048 control chromosomes in the GnomAD database, including 26,076 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 0.55 ( 26076 hom., cov: 32)

Consequence

GRIK1
NM_001330994.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.249

Publications

9 publications found
Variant links:
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]
GRIK1-AS2 (HGNC:1282): (GRIK1 antisense RNA 2)

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.861 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GRIK1NM_001330994.2 linkc.1099-13018G>C intron_variant Intron 7 of 17 ENST00000327783.9 NP_001317923.1 E7ENK3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GRIK1ENST00000327783.9 linkc.1099-13018G>C intron_variant Intron 7 of 17 5 NM_001330994.2 ENSP00000327687.4 E7ENK3

Frequencies

GnomAD3 genomes
AF:
0.546
AC:
82995
AN:
151928
Hom.:
26021
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.868
Gnomad AMI
AF:
0.366
Gnomad AMR
AF:
0.500
Gnomad ASJ
AF:
0.325
Gnomad EAS
AF:
0.621
Gnomad SAS
AF:
0.501
Gnomad FIN
AF:
0.431
Gnomad MID
AF:
0.392
Gnomad NFE
AF:
0.392
Gnomad OTH
AF:
0.500
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.547
AC:
83111
AN:
152048
Hom.:
26076
Cov.:
32
AF XY:
0.547
AC XY:
40602
AN XY:
74286
show subpopulations
African (AFR)
AF:
0.869
AC:
36068
AN:
41522
American (AMR)
AF:
0.500
AC:
7627
AN:
15266
Ashkenazi Jewish (ASJ)
AF:
0.325
AC:
1129
AN:
3472
East Asian (EAS)
AF:
0.621
AC:
3202
AN:
5160
South Asian (SAS)
AF:
0.501
AC:
2412
AN:
4814
European-Finnish (FIN)
AF:
0.431
AC:
4541
AN:
10548
Middle Eastern (MID)
AF:
0.398
AC:
117
AN:
294
European-Non Finnish (NFE)
AF:
0.392
AC:
26629
AN:
67952
Other (OTH)
AF:
0.499
AC:
1053
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1606
3212
4817
6423
8029
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
676
1352
2028
2704
3380
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.487
Hom.:
2504
Bravo
AF:
0.566
Asia WGS
AF:
0.620
AC:
2156
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
2.5
DANN
Benign
0.43
PhyloP100
0.25
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

Publications

Other links and lift over

dbSNP: rs363449; hg19: chr21-30984275; API