rs12098567

chr10-86314017-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_017551.3(GRID1):c.235+49924A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0663 in 152,280 control chromosomes in the GnomAD database, including 922 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 0.066 (922 hom., cov: 33)
• Consequence: GRID1 NM_017551.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.36

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.28).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GRID1	NM_017551.3	c.235+49924A>G		intron_variant		ENST00000327946.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GRID1	ENST00000327946.12	c.235+49924A>G		intron_variant		2	NM_017551.3	P1
GRID1	ENST00000464741.2	c.235+49924A>G		intron_variant, NMD_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.0663 AC: 10082 AN: 152162 Hom.: 918 Cov.: 33

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0275

Gnomad ASJ AF: 0.0234

Gnomad EAS AF: 0.0144

Gnomad SAS AF: 0.00724

Gnomad FIN AF: 0.000565

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.00750

Gnomad OTH AF: 0.0516

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

GnomAD4 genome AF: 0.0663 AC: 10103 AN: 152280 Hom.: 922 Cov.: 33 AF XY: 0.0638 AC XY: 4753 AN XY: 74476

Gnomad4 AFR AF: 0.213

Gnomad4 AMR AF: 0.0275

Gnomad4 ASJ AF: 0.0234

Gnomad4 EAS AF: 0.0139

Gnomad4 SAS AF: 0.00704

Gnomad4 FIN AF: 0.000565

Gnomad4 NFE AF: 0.00750

Gnomad4 OTH AF: 0.0510

Alfa AF: 0.0182 Hom.: 145

Bravo AF: 0.0740

Asia WGS AF: 0.0300 AC: 106 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.28
Cadd	Benign	18
Dann	Benign	0.90

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: rs12098567; hg19: chr10-88073774;