10-86200054-C-T

Variant names:

• chr10-86200054-C-T
• rs999383
• NM_017551.3:c.520+6310G>A

Variant summary

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

The NM_017551.3(GRID1):​c.520+6310G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.416 in 150,332 control chromosomes in the GnomAD database, including 14,001 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 0.42 (14001 hom., cov: 30)
• Consequence: GRID1 NM_017551.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.251
• Publications: 2 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.567 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GRID1	NM_017551.3	MANE Select	c.520+6310G>A		intron	N/A	NP_060021.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GRID1	ENST00000327946.12	TSL:2 MANE Select	c.520+6310G>A		intron	N/A	ENSP00000330148.7
	GRID1	ENST00000464741.2	TSL:1	n.520+6310G>A		intron	N/A	ENSP00000433064.1

Frequencies

GnomAD3 genomes AF: 0.416 AC: 62444 AN: 150218 Hom.: 13958 Cov.: 30

Gnomad AFR AF: 0.555

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.508

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.395

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.416 AC: 62551 AN: 150332 Hom.: 14001 Cov.: 30 AF XY: 0.418 AC XY: 30760 AN XY: 73506

African (AFR) AF: 0.555 AC: 22877 AN: 41222

American (AMR) AF: 0.387 AC: 5875 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.375 AC: 1297 AN: 3458

East Asian (EAS) AF: 0.584 AC: 2983 AN: 5106

South Asian (SAS) AF: 0.510 AC: 2443 AN: 4792

European-Finnish (FIN) AF: 0.385 AC: 4032 AN: 10468

Middle Eastern (MID) AF: 0.411 AC: 120 AN: 292

European-Non Finnish (NFE) AF: 0.326 AC: 21798 AN: 66810

Other (OTH) AF: 0.388 AC: 813 AN: 2094

Alfa AF: 0.358 Hom.: 2811

Bravo AF: 0.418

Asia WGS AF: 0.540 AC: 1877 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.1
DANN	Benign	0.79
PhyloP100		0.25
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: rs999383; hg19: chr10-87959811;