rs881343

Variant summary

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

The NM_017551.3(GRID1):​c.521-23365G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,064 control chromosomes in the GnomAD database, including 1,652 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 0.14 ( 1652 hom., cov: 32)

Consequence

GRID1
NM_017551.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.577
Variant links:
Genes affected
GRID1 (HGNC:4575): (glutamate ionotropic receptor delta type subunit 1) This gene encodes a subunit of glutamate receptor channels. These channels mediate most of the fast excitatory synaptic transmission in the central nervous system and play key roles in synaptic plasticity.[provided by RefSeq, Jan 2009]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
GRID1NM_017551.3 linkuse as main transcriptc.521-23365G>A intron_variant ENST00000327946.12

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
GRID1ENST00000327946.12 linkuse as main transcriptc.521-23365G>A intron_variant 2 NM_017551.3 P1Q9ULK0-1
GRID1ENST00000464741.2 linkuse as main transcriptc.521-23365G>A intron_variant, NMD_transcript_variant 1

Frequencies

GnomAD3 genomes
AF:
0.140
AC:
21348
AN:
151944
Hom.:
1632
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.164
Gnomad AMI
AF:
0.0868
Gnomad AMR
AF:
0.201
Gnomad ASJ
AF:
0.157
Gnomad EAS
AF:
0.201
Gnomad SAS
AF:
0.165
Gnomad FIN
AF:
0.107
Gnomad MID
AF:
0.225
Gnomad NFE
AF:
0.110
Gnomad OTH
AF:
0.155
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.141
AC:
21422
AN:
152064
Hom.:
1652
Cov.:
32
AF XY:
0.144
AC XY:
10693
AN XY:
74348
show subpopulations
Gnomad4 AFR
AF:
0.165
Gnomad4 AMR
AF:
0.202
Gnomad4 ASJ
AF:
0.157
Gnomad4 EAS
AF:
0.200
Gnomad4 SAS
AF:
0.164
Gnomad4 FIN
AF:
0.107
Gnomad4 NFE
AF:
0.110
Gnomad4 OTH
AF:
0.159
Alfa
AF:
0.122
Hom.:
323
Bravo
AF:
0.150
Asia WGS
AF:
0.229
AC:
796
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
1.2
DANN
Benign
0.53

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: rs881343; hg19: chr10-87922146; API