rs11591408

Variant names:

• chr10-86226152-T-C
• rs11591408
• NM_017551.3:c.236-19504A>G

Your query was ambiguous. Multiple possible variants found:

• chr10-86226152-T-C
• chr10-86226152-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.323
• Publications: 1 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017551.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GRID1	NM_017551.3	MANE Select	c.236-19504A>G		intron	N/A	NP_060021.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GRID1	ENST00000327946.12	TSL:2 MANE Select	c.236-19504A>G		intron	N/A	ENSP00000330148.7
	GRID1	ENST00000464741.2	TSL:1	n.236-19504A>G		intron	N/A	ENSP00000433064.1

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47430 AN: 151684 Hom.: 7844 Cov.: 31

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

African (AFR) AF: 0.228 AC: 9443 AN: 41348

American (AMR) AF: 0.301 AC: 4595 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.321 AC: 1113 AN: 3468

East Asian (EAS) AF: 0.300 AC: 1540 AN: 5140

South Asian (SAS) AF: 0.181 AC: 871 AN: 4812

European-Finnish (FIN) AF: 0.263 AC: 2785 AN: 10590

Middle Eastern (MID) AF: 0.284 AC: 83 AN: 292

European-Non Finnish (NFE) AF: 0.381 AC: 25857 AN: 67854

Other (OTH) AF: 0.346 AC: 729 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.6
DANN	Benign	0.40
PhyloP100		-0.32
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

Other links and lift over

dbSNP: rs11591408; hg19: chr10-87985909;