rs524874

Positions:

• chr11-88979215-A-G

Variant summary

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

The NM_001143831.3(GRM5):​c.661+67997T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.615 in 152,006 control chromosomes in the GnomAD database, including 30,258 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 0.62 (30258 hom., cov: 31)
• Consequence: GRM5 NM_001143831.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41

Genes affected

GRM5 (HGNC:4597): (glutamate metabotropic receptor 5) This gene encodes a member of the G-protein coupled receptor 3 protein family. The encoded protein is a metabatropic glutamate receptor, whose signaling activates a phosphatidylinositol-calcium second messenger system. This protein may be involved in the regulation of neural network activity and synaptic plasticity. Glutamatergic neurotransmission is involved in most aspects of normal brain function and can be perturbed in many neuropathologic conditions. A pseudogene of this gene has been defined on chromosome 11. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2014]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.817 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GRM5	NM_001143831.3	c.661+67997T>C		intron_variant		ENST00000305447.5
GRM5	NM_000842.5	c.661+67997T>C		intron_variant
GRM5	NM_001384268.1	c.661+67997T>C		intron_variant
GRM5	XM_011542792.2	c.661+67997T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GRM5	ENST00000305447.5	c.661+67997T>C		intron_variant		1	NM_001143831.3	A2
GRM5	ENST00000305432.9	c.661+67997T>C		intron_variant		1		P2
GRM5	ENST00000449371.6	c.223+29820T>C		intron_variant		3
GRM5	ENST00000455756.6	c.661+67997T>C		intron_variant		2		P2

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93396 AN: 151888 Hom.: 30212 Cov.: 31

Gnomad AFR AF: 0.825

Gnomad AMI AF: 0.668

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.537

Gnomad SAS AF: 0.665

Gnomad FIN AF: 0.421

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.613

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

GnomAD4 genome AF: 0.615 AC: 93496 AN: 152006 Hom.: 30258 Cov.: 31 AF XY: 0.610 AC XY: 45288 AN XY: 74302

Gnomad4 AFR AF: 0.825

Gnomad4 AMR AF: 0.578

Gnomad4 ASJ AF: 0.550

Gnomad4 EAS AF: 0.537

Gnomad4 SAS AF: 0.665

Gnomad4 FIN AF: 0.421

Gnomad4 NFE AF: 0.531

Gnomad4 OTH AF: 0.610

Alfa AF: 0.570 Hom.: 3197

Bravo AF: 0.635

Asia WGS AF: 0.623 AC: 2167 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.29
DANN	Benign	0.57

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: rs524874; hg19: chr11-88712383;