10-85934535-T-C

Variant names:

• chr10-85934535-T-C
• rs76765968
• NM_017551.3:c.727-18296A>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.727-18296A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0973 in 151,994 control chromosomes in the GnomAD database, including 872 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 0.097 (872 hom., cov: 31)
• Consequence: GRID1 NM_017551.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 6 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017551.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GRID1	NM_017551.3	MANE Select	c.727-18296A>G		intron	N/A	NP_060021.1	Q9ULK0-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GRID1	ENST00000327946.12	TSL:2 MANE Select	c.727-18296A>G		intron	N/A	ENSP00000330148.7	Q9ULK0-1
	GRID1	ENST00000464741.2	TSL:1	n.727-18296A>G		intron	N/A	ENSP00000433064.1	G3V186

Frequencies

GnomAD3 genomes AF: 0.0974 AC: 14786 AN: 151876 Hom.: 872 Cov.: 31

Gnomad AFR AF: 0.0435

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.00638

Gnomad SAS AF: 0.0913

Gnomad FIN AF: 0.0990

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.0973 AC: 14785 AN: 151994 Hom.: 872 Cov.: 31 AF XY: 0.0959 AC XY: 7126 AN XY: 74290

African (AFR) AF: 0.0434 AC: 1800 AN: 41462

American (AMR) AF: 0.105 AC: 1607 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 450 AN: 3466

East Asian (EAS) AF: 0.00601 AC: 31 AN: 5158

South Asian (SAS) AF: 0.0910 AC: 437 AN: 4802

European-Finnish (FIN) AF: 0.0990 AC: 1046 AN: 10564

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.134 AC: 9128 AN: 67966

Other (OTH) AF: 0.104 AC: 218 AN: 2104

Alfa AF: 0.111 Hom.: 2008

Bravo AF: 0.0948

Asia WGS AF: 0.0410 AC: 143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.093
DANN	Benign	0.70
PhyloP100		-1.0
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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs76765968;

hg19: chr10-87694292;