NM_014619.5:c.1476+7167A>G
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_014619.5(GRIK4):c.1476+7167A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.074 in 152,276 control chromosomes in the GnomAD database, including 517 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 0.074 ( 517 hom., cov: 31)
Consequence
GRIK4
NM_014619.5 intron
NM_014619.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0490
Publications
3 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]
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=-0.86).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GRIK4 | NM_014619.5 | c.1476+7167A>G | intron_variant | Intron 13 of 20 | ENST00000527524.8 | NP_055434.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GRIK4 | ENST00000527524.8 | c.1476+7167A>G | intron_variant | Intron 13 of 20 | 2 | NM_014619.5 | ENSP00000435648.2 | |||
GRIK4 | ENST00000438375.2 | c.1476+7167A>G | intron_variant | Intron 12 of 19 | 1 | ENSP00000404063.2 | ||||
GRIK4 | ENST00000533291.5 | n.1874+7167A>G | intron_variant | Intron 13 of 17 | 1 | |||||
GRIK4 | ENST00000638419.1 | c.1476+7167A>G | intron_variant | Intron 13 of 20 | 5 | ENSP00000492086.1 |
Frequencies
GnomAD3 genomes AF: 0.0740 AC: 11256AN: 152158Hom.: 515 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
11256
AN:
152158
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0740 AC: 11261AN: 152276Hom.: 517 Cov.: 31 AF XY: 0.0754 AC XY: 5614AN XY: 74466 show subpopulations
GnomAD4 genome
AF:
AC:
11261
AN:
152276
Hom.:
Cov.:
31
AF XY:
AC XY:
5614
AN XY:
74466
show subpopulations
African (AFR)
AF:
AC:
5411
AN:
41528
American (AMR)
AF:
AC:
808
AN:
15298
Ashkenazi Jewish (ASJ)
AF:
AC:
145
AN:
3470
East Asian (EAS)
AF:
AC:
379
AN:
5186
South Asian (SAS)
AF:
AC:
454
AN:
4826
European-Finnish (FIN)
AF:
AC:
626
AN:
10622
Middle Eastern (MID)
AF:
AC:
3
AN:
294
European-Non Finnish (NFE)
AF:
AC:
3268
AN:
68028
Other (OTH)
AF:
AC:
126
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
537
1073
1610
2146
2683
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
267
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.