10-85980996-C-T

Position:

• chr10-85980996-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_017551.3(GRID1):​c.727-64757G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 152,112 control chromosomes in the GnomAD database, including 9,350 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 (9350 hom., cov: 33)
• Consequence: GRID1 NM_017551.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.139

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.483 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GRID1	NM_017551.3	c.727-64757G>A		intron_variant		ENST00000327946.12	NP_060021.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GRID1	ENST00000327946.12	c.727-64757G>A		intron_variant		2	NM_017551.3	ENSP00000330148	P1
GRID1	ENST00000464741.2	c.727-64757G>A		intron_variant, NMD_transcript_variant		1		ENSP00000433064

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50910 AN: 151996 Hom.: 9353 Cov.: 33

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.335 AC: 50915 AN: 152112 Hom.: 9350 Cov.: 33 AF XY: 0.334 AC XY: 24802 AN XY: 74340

Gnomad4 AFR AF: 0.191

Gnomad4 AMR AF: 0.326

Gnomad4 ASJ AF: 0.317

Gnomad4 EAS AF: 0.367

Gnomad4 SAS AF: 0.500

Gnomad4 FIN AF: 0.323

Gnomad4 NFE AF: 0.411

Gnomad4 OTH AF: 0.307

Alfa AF: 0.370 Hom.: 2166

Bravo AF: 0.325

Asia WGS AF: 0.391 AC: 1358 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.9
DANN	Benign	0.75

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

Publications

LitVar

Other links and lift over

dbSNP: rs10788473; hg19: chr10-87740753;