chr10-86226152-T-C

Position:

• chr10-86226152-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_017551.3(GRID1):​c.236-19504A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 151,800 control chromosomes in the GnomAD database, including 7,843 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 0.31 (7843 hom., cov: 31)
• Consequence: GRID1 NM_017551.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.323

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.377 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GRID1	NM_017551.3	c.236-19504A>G		intron_variant		ENST00000327946.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GRID1	ENST00000327946.12	c.236-19504A>G		intron_variant		2	NM_017551.3	P1
GRID1	ENST00000464741.2	c.236-19504A>G		intron_variant, NMD_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47430 AN: 151684 Hom.: 7844 Cov.: 31

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.283

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.312 AC: 47434 AN: 151800 Hom.: 7843 Cov.: 31 AF XY: 0.306 AC XY: 22703 AN XY: 74206

Gnomad4 AFR AF: 0.228

Gnomad4 AMR AF: 0.301

Gnomad4 ASJ AF: 0.321

Gnomad4 EAS AF: 0.300

Gnomad4 SAS AF: 0.181

Gnomad4 FIN AF: 0.263

Gnomad4 NFE AF: 0.381

Gnomad4 OTH AF: 0.346

Alfa AF: 0.327 Hom.: 1082

Bravo AF: 0.312

Asia WGS AF: 0.211 AC: 736 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.6
DANN	Benign	0.40

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

Publications

LitVar

Other links and lift over

dbSNP: rs11591408; hg19: chr10-87985909;