rs1917145

chr10-85748007-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.1234-18393C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0484 in 152,182 control chromosomes in the GnomAD database, including 294 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 0.048 (294 hom., cov: 32)
• Consequence: GRID1 NM_017551.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.394

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GRID1	NM_017551.3	c.1234-18393C>T		intron_variant		ENST00000327946.12
GRID1	XM_047425122.1	c.-54-18393C>T		intron_variant
GRID1	XM_047425123.1	c.-54-18393C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GRID1	ENST00000327946.12	c.1234-18393C>T		intron_variant		2	NM_017551.3	P1
GRID1	ENST00000464741.2	c.1234-18393C>T		intron_variant, NMD_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.0482 AC: 7337 AN: 152064 Hom.: 291 Cov.: 32

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.0226

Gnomad ASJ AF: 0.00922

Gnomad EAS AF: 0.0593

Gnomad SAS AF: 0.0389

Gnomad FIN AF: 0.0452

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0204

Gnomad OTH AF: 0.0378

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

GnomAD4 genome AF: 0.0484 AC: 7361 AN: 152182 Hom.: 294 Cov.: 32 AF XY: 0.0483 AC XY: 3595 AN XY: 74396

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.0225

Gnomad4 ASJ AF: 0.00922

Gnomad4 EAS AF: 0.0594

Gnomad4 SAS AF: 0.0385

Gnomad4 FIN AF: 0.0452

Gnomad4 NFE AF: 0.0204

Gnomad4 OTH AF: 0.0374

Alfa AF: 0.0237 Hom.: 88

Bravo AF: 0.0488

Asia WGS AF: 0.0500 AC: 172 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	7.7
Dann	Benign	0.70

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: rs1917145; hg19: chr10-87507764;