chr10-85609031-C-T

Position:

• chr10-85609031-C-T

Variant summary

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

The NM_017551.3(GRID1):​c.2601+4376G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.635 in 151,906 control chromosomes in the GnomAD database, including 31,686 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 0.64 (31686 hom., cov: 31)
• Consequence: GRID1 NM_017551.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.178

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]

GRID1 (HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.806 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GRID1	NM_017551.3	c.2601+4376G>A		intron_variant		ENST00000327946.12	NP_060021.1
GRID1	XM_047425122.1	c.1314+4376G>A		intron_variant			XP_047281078.1
GRID1	XM_047425123.1	c.1314+4376G>A		intron_variant			XP_047281079.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GRID1	ENST00000327946.12	c.2601+4376G>A		intron_variant		2	NM_017551.3	ENSP00000330148.7
GRID1	ENST00000464741.2	n.*166+4376G>A		intron_variant		1		ENSP00000433064.1
GRID1	ENST00000552278.2	n.78+4025G>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.635 AC: 96400 AN: 151788 Hom.: 31637 Cov.: 31

Gnomad AFR AF: 0.813

Gnomad AMI AF: 0.697

Gnomad AMR AF: 0.571

Gnomad ASJ AF: 0.640

Gnomad EAS AF: 0.414

Gnomad SAS AF: 0.587

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.573

Gnomad OTH AF: 0.628

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

GnomAD4 genome AF: 0.635 AC: 96505 AN: 151906 Hom.: 31686 Cov.: 31 AF XY: 0.633 AC XY: 46983 AN XY: 74214

Gnomad4 AFR AF: 0.813

Gnomad4 AMR AF: 0.571

Gnomad4 ASJ AF: 0.640

Gnomad4 EAS AF: 0.414

Gnomad4 SAS AF: 0.585

Gnomad4 FIN AF: 0.551

Gnomad4 NFE AF: 0.573

Gnomad4 OTH AF: 0.629

Alfa AF: 0.602 Hom.: 4921

Bravo AF: 0.643

Asia WGS AF: 0.557 AC: 1936 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	4.6
DANN	Benign	0.64

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: rs2175200; hg19: chr10-87368788; COSMIC: COSV60016987; COSMIC: COSV60016987;