rs362962

chr6-146312682-T-C

Variant summary

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

The NM_001278064.2(GRM1):c.1186+7836T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.378 in 152,138 control chromosomes in the GnomAD database, including 15,014 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 0.38 (15014 hom., cov: 32)
• Consequence: GRM1 NM_001278064.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.618

Genes affected

GRM1 (HGNC:4593): (glutamate metabotropic receptor 1) This gene encodes a metabotropic glutamate receptor that functions by activating phospholipase C. L-glutamate is the major excitatory neurotransmitter in the central nervous system and activates both ionotropic and metabotropic glutamate receptors. Glutamatergic neurotransmission is involved in most aspects of normal brain function and can be perturbed in many neuropathologic conditions. The canonical alpha isoform of the encoded protein is a disulfide-linked homodimer whose activity is mediated by a G-protein-coupled phosphatidylinositol-calcium second messenger system. This gene may be associated with many disease states, including schizophrenia, bipolar disorder, depression, and breast cancer. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, May 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.745 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GRM1	NM_001278064.2	c.1186+7836T>C		intron_variant		ENST00000282753.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GRM1	ENST00000282753.6	c.1186+7836T>C		intron_variant		1	NM_001278064.2	P1

Frequencies

GnomAD3 genomes AF: 0.378 AC: 57424 AN: 152020 Hom.: 14972 Cov.: 32

Gnomad AFR AF: 0.752

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.378 AC: 57530 AN: 152138 Hom.: 15014 Cov.: 32 AF XY: 0.374 AC XY: 27809 AN XY: 74392

Gnomad4 AFR AF: 0.752

Gnomad4 AMR AF: 0.321

Gnomad4 ASJ AF: 0.279

Gnomad4 EAS AF: 0.141

Gnomad4 SAS AF: 0.258

Gnomad4 FIN AF: 0.196

Gnomad4 NFE AF: 0.226

Gnomad4 OTH AF: 0.363

Alfa AF: 0.254 Hom.: 8825

Bravo AF: 0.405

Asia WGS AF: 0.256 AC: 890 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.74
Dann	Benign	0.64

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: rs362962; hg19: chr6-146633818;