chr10-86047633-G-A

Variant names:

• chr10-86047633-G-A
• rs10788478
• NM_017551.3:c.726+91186C>T

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+91186C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.333 in 151,728 control chromosomes in the GnomAD database, including 9,449 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 0.33 (9449 hom., cov: 31)
• Consequence: GRID1 NM_017551.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.165
• Publications: 3 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=-0.65).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.484 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.726+91186C>T		intron	N/A	NP_060021.1	Q9ULK0-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GRID1	ENST00000327946.12	TSL:2 MANE Select	c.726+91186C>T		intron	N/A	ENSP00000330148.7	Q9ULK0-1
	GRID1	ENST00000464741.2	TSL:1	n.726+91186C>T		intron	N/A	ENSP00000433064.1	G3V186

Frequencies

GnomAD3 genomes AF: 0.334 AC: 50571 AN: 151610 Hom.: 9443 Cov.: 31

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.242

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.333 AC: 50575 AN: 151728 Hom.: 9449 Cov.: 31 AF XY: 0.336 AC XY: 24930 AN XY: 74120

African (AFR) AF: 0.153 AC: 6335 AN: 41368

American (AMR) AF: 0.364 AC: 5554 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.278 AC: 963 AN: 3466

East Asian (EAS) AF: 0.411 AC: 2110 AN: 5134

South Asian (SAS) AF: 0.500 AC: 2396 AN: 4788

European-Finnish (FIN) AF: 0.409 AC: 4300 AN: 10512

Middle Eastern (MID) AF: 0.243 AC: 71 AN: 292

European-Non Finnish (NFE) AF: 0.409 AC: 27804 AN: 67904

Other (OTH) AF: 0.304 AC: 638 AN: 2102

Alfa AF: 0.378 Hom.: 19011

Bravo AF: 0.317

Asia WGS AF: 0.408 AC: 1419 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	11
DANN	Benign	0.69
PhyloP100		0.17
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: rs10788478; hg19: chr10-87807390;