rs1906953

Variant names:

• chr6-34068669-C-T
• rs1906953
• NM_000841.4:c.737-6641G>A

Variant summary

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

The NM_000841.4(GRM4):​c.737-6641G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 152,150 control chromosomes in the GnomAD database, including 6,633 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 0.25 (6633 hom., cov: 32)
• Consequence: GRM4 NM_000841.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.213
• Publications: 30 publications found

Genes affected

GRM4 (HGNC:4596): (glutamate metabotropic receptor 4) 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 metabotropic glutamate receptors are a family of G protein-coupled receptors, that have been divided into 3 groups on the basis of sequence homology, putative signal transduction mechanisms, and pharmacologic properties. Group I includes GRM1 and GRM5 and these receptors have been shown to activate phospholipase C. Group II includes GRM2 and GRM3 while Group III includes GRM4, GRM6, GRM7 and GRM8. Group II and III receptors are linked to the inhibition of the cyclic AMP cascade but differ in their agonist selectivities. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2012]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GRM4	NM_000841.4	c.737-6641G>A		intron_variant	Intron 3 of 10	ENST00000538487.7	NP_000832.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GRM4	ENST00000538487.7	c.737-6641G>A		intron_variant	Intron 3 of 10	2	NM_000841.4	ENSP00000440556.1

Frequencies

GnomAD3 genomes AF: 0.250 AC: 37938 AN: 152030 Hom.: 6636 Cov.: 32

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.484

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.261

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

GnomAD4 genome AF: 0.249 AC: 37947 AN: 152150 Hom.: 6633 Cov.: 32 AF XY: 0.249 AC XY: 18492 AN XY: 74382

African (AFR) AF: 0.466 AC: 19321 AN: 41490

American (AMR) AF: 0.253 AC: 3873 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 517 AN: 3468

East Asian (EAS) AF: 0.483 AC: 2493 AN: 5162

South Asian (SAS) AF: 0.224 AC: 1082 AN: 4824

European-Finnish (FIN) AF: 0.115 AC: 1223 AN: 10616

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.129 AC: 8751 AN: 67992

Other (OTH) AF: 0.260 AC: 548 AN: 2110

Alfa AF: 0.167 Hom.: 8869

Bravo AF: 0.273

Asia WGS AF: 0.362 AC: 1256 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.9
DANN	Benign	0.70
PhyloP100		0.21
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: rs1906953; hg19: chr6-34036446; COSMIC: COSV65214968;