10-86083248-T-G

Variant names:

• chr10-86083248-T-G
• rs7912496
• NM_017551.3:c.726+55571A>C

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+55571A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.786 in 152,080 control chromosomes in the GnomAD database, including 48,054 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 0.79 (48054 hom., cov: 32)
• Consequence: GRID1 NM_017551.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.243
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.862 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+55571A>C		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+55571A>C		intron	N/A	ENSP00000330148.7	Q9ULK0-1
	GRID1	ENST00000464741.2	TSL:1	n.726+55571A>C		intron	N/A	ENSP00000433064.1	G3V186

Frequencies

GnomAD3 genomes AF: 0.786 AC: 119461 AN: 151964 Hom.: 48024 Cov.: 32

Gnomad AFR AF: 0.601

Gnomad AMI AF: 0.873

Gnomad AMR AF: 0.791

Gnomad ASJ AF: 0.878

Gnomad EAS AF: 0.883

Gnomad SAS AF: 0.754

Gnomad FIN AF: 0.903

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.868

Gnomad OTH AF: 0.789

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

GnomAD4 genome AF: 0.786 AC: 119543 AN: 152080 Hom.: 48054 Cov.: 32 AF XY: 0.789 AC XY: 58675 AN XY: 74352

African (AFR) AF: 0.601 AC: 24899 AN: 41412

American (AMR) AF: 0.791 AC: 12086 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.878 AC: 3048 AN: 3470

East Asian (EAS) AF: 0.883 AC: 4574 AN: 5178

South Asian (SAS) AF: 0.755 AC: 3644 AN: 4826

European-Finnish (FIN) AF: 0.903 AC: 9564 AN: 10596

Middle Eastern (MID) AF: 0.789 AC: 232 AN: 294

European-Non Finnish (NFE) AF: 0.868 AC: 59036 AN: 68008

Other (OTH) AF: 0.787 AC: 1664 AN: 2114

Alfa AF: 0.832 Hom.: 24144

Bravo AF: 0.774

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.43
PhyloP100		-0.24
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: rs7912496; hg19: chr10-87843005;