chr10-86338038-G-A

Variant names:

• chr10-86338038-G-A
• rs11201985
• NM_017551.3:c.235+25903C>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.235+25903C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 152,044 control chromosomes in the GnomAD database, including 10,850 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 0.35 (10850 hom., cov: 32)
• Consequence: GRID1 NM_017551.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.725
• Publications: 3 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 (AMR) allele frequency at 95% confidence interval = 0.485 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GRID1	NM_017551.3	MANE Select	c.235+25903C>T		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.235+25903C>T		intron	N/A	ENSP00000330148.7
	GRID1	ENST00000464741.2	TSL:1	n.235+25903C>T		intron	N/A	ENSP00000433064.1

Frequencies

GnomAD3 genomes AF: 0.352 AC: 53403 AN: 151926 Hom.: 10850 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.351 AC: 53410 AN: 152044 Hom.: 10850 Cov.: 32 AF XY: 0.353 AC XY: 26259 AN XY: 74304

African (AFR) AF: 0.154 AC: 6380 AN: 41510

American (AMR) AF: 0.494 AC: 7552 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.312 AC: 1084 AN: 3470

East Asian (EAS) AF: 0.260 AC: 1334 AN: 5136

South Asian (SAS) AF: 0.213 AC: 1026 AN: 4812

European-Finnish (FIN) AF: 0.449 AC: 4741 AN: 10556

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.442 AC: 30074 AN: 67970

Other (OTH) AF: 0.373 AC: 785 AN: 2106

Alfa AF: 0.403 Hom.: 3162

Bravo AF: 0.351

Asia WGS AF: 0.245 AC: 850 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.35
DANN	Benign	0.51
PhyloP100		-0.72
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: rs11201985; hg19: chr10-88097795;