rs1917138

Positions:

• chr10-85757552-A-C
• chr10-85757552-A-G
• chr10-85757552-A-T

Variant summary

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

The NM_017551.3(GRID1):​c.1234-27938T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.684 in 151,634 control chromosomes in the GnomAD database, including 35,748 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 0.68 (35748 hom., cov: 33)
• Consequence: GRID1 NM_017551.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22

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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.85 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GRID1	NM_017551.3	c.1234-27938T>G		intron_variant		ENST00000327946.12
GRID1	XM_047425122.1	c.-54-27938T>G		intron_variant
GRID1	XM_047425123.1	c.-54-27938T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GRID1	ENST00000327946.12	c.1234-27938T>G		intron_variant		2	NM_017551.3	P1
GRID1	ENST00000464741.2	c.1234-27938T>G		intron_variant, NMD_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.684 AC: 103682 AN: 151516 Hom.: 35710 Cov.: 33

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.731

Gnomad AMR AF: 0.741

Gnomad ASJ AF: 0.694

Gnomad EAS AF: 0.872

Gnomad SAS AF: 0.798

Gnomad FIN AF: 0.666

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.682

Gnomad OTH AF: 0.689

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

GnomAD4 genome AF: 0.684 AC: 103779 AN: 151634 Hom.: 35748 Cov.: 33 AF XY: 0.688 AC XY: 50953 AN XY: 74098

Gnomad4 AFR AF: 0.634

Gnomad4 AMR AF: 0.741

Gnomad4 ASJ AF: 0.694

Gnomad4 EAS AF: 0.872

Gnomad4 SAS AF: 0.799

Gnomad4 FIN AF: 0.666

Gnomad4 NFE AF: 0.682

Gnomad4 OTH AF: 0.690

Alfa AF: 0.643 Hom.: 4567

Bravo AF: 0.684

Asia WGS AF: 0.802 AC: 2789 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.64
DANN	Benign	0.74

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: rs1917138; hg19: chr10-87517309;