10-86052826-T-C

Variant names:

• chr10-86052826-T-C
• rs1986558
• NM_017551.3:c.726+85993A>G

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+85993A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0866 in 152,294 control chromosomes in the GnomAD database, including 609 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 0.087 (609 hom., cov: 33)
• Consequence: GRID1 NM_017551.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.963
• Publications: 0 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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GRID1	NM_017551.3	c.726+85993A>G		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+85993A>G		intron_variant	Intron 4 of 15	2	NM_017551.3	ENSP00000330148.7
GRID1	ENST00000464741.2	n.726+85993A>G		intron_variant	Intron 4 of 14	1		ENSP00000433064.1

Frequencies

GnomAD3 genomes AF: 0.0866 AC: 13184 AN: 152176 Hom.: 608 Cov.: 33

Gnomad AFR AF: 0.0740

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.0696

Gnomad ASJ AF: 0.0620

Gnomad EAS AF: 0.000961

Gnomad SAS AF: 0.0190

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.0889

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

GnomAD4 genome AF: 0.0866 AC: 13183 AN: 152294 Hom.: 609 Cov.: 33 AF XY: 0.0843 AC XY: 6277 AN XY: 74458

African (AFR) AF: 0.0739 AC: 3071 AN: 41550

American (AMR) AF: 0.0694 AC: 1061 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0620 AC: 215 AN: 3470

East Asian (EAS) AF: 0.000963 AC: 5 AN: 5192

South Asian (SAS) AF: 0.0195 AC: 94 AN: 4830

European-Finnish (FIN) AF: 0.111 AC: 1176 AN: 10614

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7278 AN: 68024

Other (OTH) AF: 0.0880 AC: 186 AN: 2114

Alfa AF: 0.0975 Hom.: 401

Bravo AF: 0.0846

Asia WGS AF: 0.0170 AC: 60 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.6
DANN	Benign	0.84
PhyloP100		0.96
Mutation Taster		=99/1	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: rs1986558; hg19: chr10-87812583;