10-85902354-G-C

Variant names:

• chr10-85902354-G-C
• rs2222546
• NM_017551.3:c.780+13832C>G

Variant summary

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

The ENST00000327946.12(GRID1):​c.780+13832C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.362 in 152,084 control chromosomes in the GnomAD database, including 10,934 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 0.36 (10934 hom., cov: 32)
• Consequence: GRID1 ENST00000327946.12 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43
• Publications: 1 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=-1.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.516 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000327946.12. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GRID1	NM_017551.3	MANE Select	c.780+13832C>G		intron	N/A	NP_060021.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GRID1	ENST00000327946.12	TSL:2 MANE Select	c.780+13832C>G		intron	N/A	ENSP00000330148.7
	GRID1	ENST00000464741.2	TSL:1	n.780+13832C>G		intron	N/A	ENSP00000433064.1

Frequencies

GnomAD3 genomes AF: 0.362 AC: 54999 AN: 151966 Hom.: 10925 Cov.: 32

Gnomad AFR AF: 0.522

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.362 AC: 55040 AN: 152084 Hom.: 10934 Cov.: 32 AF XY: 0.360 AC XY: 26746 AN XY: 74350

African (AFR) AF: 0.522 AC: 21621 AN: 41452

American (AMR) AF: 0.329 AC: 5029 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 1316 AN: 3468

East Asian (EAS) AF: 0.197 AC: 1020 AN: 5182

South Asian (SAS) AF: 0.323 AC: 1560 AN: 4824

European-Finnish (FIN) AF: 0.249 AC: 2639 AN: 10590

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.305 AC: 20700 AN: 67962

Other (OTH) AF: 0.380 AC: 801 AN: 2110

Alfa AF: 0.192 Hom.: 380

Bravo AF: 0.375

Asia WGS AF: 0.273 AC: 951 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.094
DANN	Benign	0.41
PhyloP100		-1.4
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: rs2222546; hg19: chr10-87662111;