11-88736075-A-T

Variant names:

• chr11-88736075-A-T
• rs2892293
• NM_001143831.3:c.912-82672T>A

Variant summary

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

The NM_001143831.3(GRM5):​c.912-82672T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 152,068 control chromosomes in the GnomAD database, including 1,531 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 0.12 (1531 hom., cov: 32)
• Consequence: GRM5 NM_001143831.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.392
• Publications: 1 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GRM5	NM_001143831.3	c.912-82672T>A		intron_variant	Intron 3 of 9	ENST00000305447.5	NP_001137303.1
GRM5	NM_000842.5	c.912-82672T>A		intron_variant	Intron 3 of 8		NP_000833.1
GRM5	NM_001384268.1	c.912-82672T>A		intron_variant	Intron 3 of 8		NP_001371197.1
GRM5	XM_011542792.2	c.912-82672T>A		intron_variant	Intron 3 of 9		XP_011541094.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GRM5	ENST00000305447.5	c.912-82672T>A		intron_variant	Intron 3 of 9	1	NM_001143831.3	ENSP00000306138.4
GRM5	ENST00000305432.9	c.912-82672T>A		intron_variant	Intron 2 of 7	1		ENSP00000305905.5
GRM5	ENST00000455756.6	c.912-82672T>A		intron_variant	Intron 3 of 8	2		ENSP00000405690.2

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18736 AN: 151950 Hom.: 1533 Cov.: 32

Gnomad AFR AF: 0.0340

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.0134

Gnomad SAS AF: 0.0729

Gnomad FIN AF: 0.0854

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.123 AC: 18726 AN: 152068 Hom.: 1531 Cov.: 32 AF XY: 0.118 AC XY: 8802 AN XY: 74326

African (AFR) AF: 0.0339 AC: 1408 AN: 41530

American (AMR) AF: 0.135 AC: 2057 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 858 AN: 3466

East Asian (EAS) AF: 0.0132 AC: 68 AN: 5152

South Asian (SAS) AF: 0.0728 AC: 351 AN: 4824

European-Finnish (FIN) AF: 0.0854 AC: 906 AN: 10608

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.185 AC: 12559 AN: 67920

Other (OTH) AF: 0.157 AC: 332 AN: 2112

Alfa AF: 0.0735 Hom.: 91

Bravo AF: 0.125

Asia WGS AF: 0.0440 AC: 153 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.96
DANN	Benign	0.76
PhyloP100		-0.39
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: rs2892293; hg19: chr11-88469243;