chr10-86064481-G-A

Variant names:

• chr10-86064481-G-A
• rs10887554
• NM_017551.3:c.726+74338C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_017551.3(GRID1):​c.726+74338C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.461 in 152,138 control chromosomes in the GnomAD database, including 17,619 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 0.46 (17619 hom., cov: 33)
• Consequence: GRID1 NM_017551.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.145
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GRID1	NM_017551.3	c.726+74338C>T		intron_variant	Intron 4 of 15	ENST00000327946.12	NP_060021.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GRID1	ENST00000327946.12	c.726+74338C>T		intron_variant	Intron 4 of 15	2	NM_017551.3	ENSP00000330148.7
GRID1	ENST00000464741.2	n.726+74338C>T		intron_variant	Intron 4 of 14	1		ENSP00000433064.1

Frequencies

GnomAD3 genomes AF: 0.461 AC: 70126 AN: 152020 Hom.: 17604 Cov.: 33

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.551

Gnomad AMR AF: 0.505

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.688

Gnomad SAS AF: 0.713

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.528

Gnomad OTH AF: 0.442

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

GnomAD4 genome AF: 0.461 AC: 70157 AN: 152138 Hom.: 17619 Cov.: 33 AF XY: 0.471 AC XY: 35042 AN XY: 74382

African (AFR) AF: 0.254 AC: 10546 AN: 41518

American (AMR) AF: 0.506 AC: 7732 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.420 AC: 1458 AN: 3472

East Asian (EAS) AF: 0.689 AC: 3571 AN: 5182

South Asian (SAS) AF: 0.714 AC: 3444 AN: 4826

European-Finnish (FIN) AF: 0.564 AC: 5962 AN: 10576

Middle Eastern (MID) AF: 0.373 AC: 109 AN: 292

European-Non Finnish (NFE) AF: 0.528 AC: 35916 AN: 67970

Other (OTH) AF: 0.436 AC: 920 AN: 2108

Alfa AF: 0.499 Hom.: 32901

Bravo AF: 0.439

Asia WGS AF: 0.637 AC: 2213 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.5
DANN	Benign	0.46
PhyloP100		-0.14
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10887554; hg19: chr10-87824238;