rs11591408

Variant summary

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

The NM_017551.3(GRID1):​c.236-19504A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 151,800 control chromosomes in the GnomAD database, including 7,843 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 0.31 ( 7843 hom., cov: 31)

Consequence

GRID1
NM_017551.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.323
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=-1.01).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.377 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
GRID1NM_017551.3 linkuse as main transcriptc.236-19504A>G intron_variant ENST00000327946.12

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
GRID1ENST00000327946.12 linkuse as main transcriptc.236-19504A>G intron_variant 2 NM_017551.3 P1Q9ULK0-1
GRID1ENST00000464741.2 linkuse as main transcriptc.236-19504A>G intron_variant, NMD_transcript_variant 1

Frequencies

GnomAD3 genomes
AF:
0.313
AC:
47430
AN:
151684
Hom.:
7844
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.228
Gnomad AMI
AF:
0.459
Gnomad AMR
AF:
0.301
Gnomad ASJ
AF:
0.321
Gnomad EAS
AF:
0.301
Gnomad SAS
AF:
0.181
Gnomad FIN
AF:
0.263
Gnomad MID
AF:
0.283
Gnomad NFE
AF:
0.381
Gnomad OTH
AF:
0.350
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.312
AC:
47434
AN:
151800
Hom.:
7843
Cov.:
31
AF XY:
0.306
AC XY:
22703
AN XY:
74206
show subpopulations
Gnomad4 AFR
AF:
0.228
Gnomad4 AMR
AF:
0.301
Gnomad4 ASJ
AF:
0.321
Gnomad4 EAS
AF:
0.300
Gnomad4 SAS
AF:
0.181
Gnomad4 FIN
AF:
0.263
Gnomad4 NFE
AF:
0.381
Gnomad4 OTH
AF:
0.346
Alfa
AF:
0.327
Hom.:
1082
Bravo
AF:
0.312
Asia WGS
AF:
0.211
AC:
736
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
2.6
DANN
Benign
0.40

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: rs11591408; hg19: chr10-87985909; API