rs7899106

Variant names:

• chr10-85651147-A-G
• rs7899106
• NM_017551.3:c.1998-3750T>C

Variant summary

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

The NM_017551.3(GRID1):​c.1998-3750T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0668 in 152,266 control chromosomes in the GnomAD database, including 428 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 0.067 (428 hom., cov: 33)
• Consequence: GRID1 NM_017551.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.266

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.119 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GRID1	NM_017551.3	c.1998-3750T>C		intron_variant	Intron 12 of 15	ENST00000327946.12	NP_060021.1
GRID1	XM_047425122.1	c.711-3750T>C		intron_variant	Intron 5 of 8		XP_047281078.1
GRID1	XM_047425123.1	c.711-3750T>C		intron_variant	Intron 5 of 8		XP_047281079.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GRID1	ENST00000327946.12	c.1998-3750T>C		intron_variant	Intron 12 of 15	2	NM_017551.3	ENSP00000330148.7
GRID1	ENST00000464741.2	n.1998-3750T>C		intron_variant	Intron 12 of 14	1		ENSP00000433064.1

Frequencies

GnomAD3 genomes AF: 0.0668 AC: 10164 AN: 152148 Hom.: 428 Cov.: 33

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.0474

Gnomad ASJ AF: 0.0611

Gnomad EAS AF: 0.00538

Gnomad SAS AF: 0.0269

Gnomad FIN AF: 0.0436

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0478

Gnomad OTH AF: 0.0627

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

GnomAD4 genome AF: 0.0668 AC: 10177 AN: 152266 Hom.: 428 Cov.: 33 AF XY: 0.0659 AC XY: 4908 AN XY: 74466

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.0474

Gnomad4 ASJ AF: 0.0611

Gnomad4 EAS AF: 0.00539

Gnomad4 SAS AF: 0.0269

Gnomad4 FIN AF: 0.0436

Gnomad4 NFE AF: 0.0478

Gnomad4 OTH AF: 0.0630

Alfa AF: 0.0524 Hom.: 64

Bravo AF: 0.0698

Asia WGS AF: 0.0260 AC: 91 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.54

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: rs7899106; hg19: chr10-87410904;