10-85848703-C-T

Variant names:

• chr10-85848703-C-T
• rs7076096
• NM_017551.3:c.1233+5793G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_017551.3(GRID1):​c.1233+5793G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.241 in 152,048 control chromosomes in the GnomAD database, including 4,737 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 0.24 (4737 hom., cov: 32)
• Consequence: GRID1 NM_017551.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.159
• 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.322 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GRID1	NM_017551.3	c.1233+5793G>A		intron_variant	Intron 8 of 15	ENST00000327946.12	NP_060021.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GRID1	ENST00000327946.12	c.1233+5793G>A		intron_variant	Intron 8 of 15	2	NM_017551.3	ENSP00000330148.7
GRID1	ENST00000464741.2	n.1233+5793G>A		intron_variant	Intron 8 of 14	1		ENSP00000433064.1

Frequencies

GnomAD3 genomes AF: 0.241 AC: 36553 AN: 151930 Hom.: 4710 Cov.: 32

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.238

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

GnomAD4 genome AF: 0.241 AC: 36627 AN: 152048 Hom.: 4737 Cov.: 32 AF XY: 0.242 AC XY: 17965 AN XY: 74312

African (AFR) AF: 0.326 AC: 13536 AN: 41464

American (AMR) AF: 0.220 AC: 3370 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.259 AC: 897 AN: 3466

East Asian (EAS) AF: 0.149 AC: 774 AN: 5186

South Asian (SAS) AF: 0.272 AC: 1311 AN: 4820

European-Finnish (FIN) AF: 0.205 AC: 2159 AN: 10550

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.203 AC: 13814 AN: 67962

Other (OTH) AF: 0.234 AC: 494 AN: 2112

Alfa AF: 0.216 Hom.: 1654

Bravo AF: 0.243

Asia WGS AF: 0.206 AC: 719 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	9.1
DANN	Benign	0.69
PhyloP100		-0.16
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: rs7076096; hg19: chr10-87608460;