NM_017551.3:c.726+31444A>G

Variant names:

• chr10-86107375-T-C
• rs11595081
• NM_017551.3:c.726+31444A>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.726+31444A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0776 in 152,268 control chromosomes in the GnomAD database, including 556 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 0.078 (556 hom., cov: 32)
• Consequence: GRID1 NM_017551.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0350
• Publications: 0 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GRID1	NM_017551.3	c.726+31444A>G		intron_variant	Intron 4 of 15	ENST00000327946.12	NP_060021.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GRID1	ENST00000327946.12	c.726+31444A>G		intron_variant	Intron 4 of 15	2	NM_017551.3	ENSP00000330148.7
GRID1	ENST00000464741.2	n.726+31444A>G		intron_variant	Intron 4 of 14	1		ENSP00000433064.1

Frequencies

GnomAD3 genomes AF: 0.0776 AC: 11802 AN: 152150 Hom.: 555 Cov.: 32

Gnomad AFR AF: 0.0915

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.0994

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.0781

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.0482

Gnomad OTH AF: 0.0759

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0776 AC: 11817 AN: 152268 Hom.: 556 Cov.: 32 AF XY: 0.0826 AC XY: 6151 AN XY: 74456

African (AFR) AF: 0.0916 AC: 3805 AN: 41554

American (AMR) AF: 0.0993 AC: 1520 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 350 AN: 3468

East Asian (EAS) AF: 0.145 AC: 750 AN: 5166

South Asian (SAS) AF: 0.210 AC: 1012 AN: 4818

European-Finnish (FIN) AF: 0.0781 AC: 830 AN: 10622

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.0482 AC: 3276 AN: 68016

Other (OTH) AF: 0.0766 AC: 162 AN: 2116

Alfa AF: 0.0651 Hom.: 57

Bravo AF: 0.0782

Asia WGS AF: 0.187 AC: 650 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.57
PhyloP100		0.035
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: rs11595081; hg19: chr10-87867132;