chr10-86014640-G-A

Position:

• chr10-86014640-G-A

Variant summary

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

The NM_017551.3(GRID1):​c.727-98401C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 152,080 control chromosomes in the GnomAD database, including 8,990 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 (8990 hom., cov: 33)
• Consequence: GRID1 NM_017551.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.810

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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GRID1	NM_017551.3	c.727-98401C>T		intron_variant		ENST00000327946.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GRID1	ENST00000327946.12	c.727-98401C>T		intron_variant		2	NM_017551.3	P1
GRID1	ENST00000464741.2	c.727-98401C>T		intron_variant, NMD_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.330 AC: 50154 AN: 151960 Hom.: 8986 Cov.: 33

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.330 AC: 50164 AN: 152080 Hom.: 8990 Cov.: 33 AF XY: 0.331 AC XY: 24575 AN XY: 74316

Gnomad4 AFR AF: 0.186

Gnomad4 AMR AF: 0.368

Gnomad4 ASJ AF: 0.287

Gnomad4 EAS AF: 0.385

Gnomad4 SAS AF: 0.492

Gnomad4 FIN AF: 0.332

Gnomad4 NFE AF: 0.395

Gnomad4 OTH AF: 0.300

Alfa AF: 0.373 Hom.: 22534

Bravo AF: 0.322

Asia WGS AF: 0.404 AC: 1405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.1
DANN	Benign	0.53

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: rs10887549; hg19: chr10-87774397;