rs10502239

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_014619.5(GRIK4):​c.-158-32543A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0716 in 152,272 control chromosomes in the GnomAD database, including 1,328 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 0.072 ( 1328 hom., cov: 32)

Consequence

GRIK4
NM_014619.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.06
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 = 0.24 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
GRIK4NM_014619.5 linkuse as main transcriptc.-158-32543A>G intron_variant ENST00000527524.8 NP_055434.2 Q16099A0A8D9PH79
GRIK4NM_001282470.3 linkuse as main transcriptc.-50-39127A>G intron_variant NP_001269399.1 Q16099A0A8D9PH79B2RAP6
GRIK4NM_001282473.3 linkuse as main transcriptc.-158-32543A>G intron_variant NP_001269402.1 A6H8K8B2RAP6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
GRIK4ENST00000527524.8 linkuse as main transcriptc.-158-32543A>G intron_variant 2 NM_014619.5 ENSP00000435648.2 Q16099

Frequencies

GnomAD3 genomes
AF:
0.0714
AC:
10865
AN:
152154
Hom.:
1322
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.244
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0326
Gnomad ASJ
AF:
0.00231
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00104
Gnomad FIN
AF:
0.000471
Gnomad MID
AF:
0.0253
Gnomad NFE
AF:
0.00160
Gnomad OTH
AF:
0.0603
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0716
AC:
10905
AN:
152272
Hom.:
1328
Cov.:
32
AF XY:
0.0690
AC XY:
5135
AN XY:
74466
show subpopulations
Gnomad4 AFR
AF:
0.244
Gnomad4 AMR
AF:
0.0325
Gnomad4 ASJ
AF:
0.00231
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00104
Gnomad4 FIN
AF:
0.000471
Gnomad4 NFE
AF:
0.00160
Gnomad4 OTH
AF:
0.0597
Alfa
AF:
0.0460
Hom.:
113
Bravo
AF:
0.0814
Asia WGS
AF:
0.0180
AC:
64
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
0.54
DANN
Benign
0.67

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs10502239; hg19: chr11-120491851; API