rs7895098

chr10-85890621-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.781-21441C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.214 in 151,996 control chromosomes in the GnomAD database, including 3,684 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 0.21 (3684 hom., cov: 32)
• Consequence: GRID1 NM_017551.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30

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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.276 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GRID1	NM_017551.3	c.781-21441C>T		intron_variant		ENST00000327946.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GRID1	ENST00000327946.12	c.781-21441C>T		intron_variant		2	NM_017551.3	P1
GRID1	ENST00000464741.2	c.781-21441C>T		intron_variant, NMD_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.214 AC: 32505 AN: 151878 Hom.: 3671 Cov.: 32

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.242

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.214 AC: 32544 AN: 151996 Hom.: 3684 Cov.: 32 AF XY: 0.213 AC XY: 15821 AN XY: 74294

Gnomad4 AFR AF: 0.280

Gnomad4 AMR AF: 0.204

Gnomad4 ASJ AF: 0.237

Gnomad4 EAS AF: 0.206

Gnomad4 SAS AF: 0.226

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.228

Alfa AF: 0.195 Hom.: 1437

Bravo AF: 0.223

Asia WGS AF: 0.238 AC: 828 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.041
Dann	Benign	0.37

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: rs7895098; hg19: chr10-87650378;