rs10201627

chr2-230909662-C-Achr2-230909662-C-Gchr2-230909662-C-T

Variant summary

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

The NM_005683.4(GPR55):c.*341G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0696 in 225,476 control chromosomes in the GnomAD database, including 1,480 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 0.086 (1332 hom., cov: 32)
  • Exomes 𝑓: 0.036 (148 hom.)
• Consequence: GPR55 NM_005683.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0580

Genes affected

GPR55 (HGNC:4511): (G protein-coupled receptor 55) This gene belongs to the G-protein-coupled receptor superfamily. The encoded integral membrane protein is a likely cannabinoid receptor. It may be involved in several physiological and pathological processes by activating a variety of signal transduction pathways. [provided by RefSeq, Aug 2013]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.231 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GPR55	NM_005683.4	c.*341G>T		3_prime_UTR_variant	2/2	ENST00000650999.1
GPR55	XM_005246952.5	c.*341G>T		3_prime_UTR_variant	2/2
GPR55	XM_011512175.4	c.*341G>T		3_prime_UTR_variant	2/2
GPR55	XM_011512176.3	c.*341G>T		3_prime_UTR_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GPR55	ENST00000650999.1	c.*341G>T		3_prime_UTR_variant	2/2		NM_005683.4	P1
	ENST00000454890.1	n.160C>A		non_coding_transcript_exon_variant	2/2	4

Frequencies

GnomAD3 genomes AF: 0.0857 AC: 13034 AN: 152050 Hom.: 1326 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0341

Gnomad ASJ AF: 0.0271

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.00179

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0178

Gnomad OTH AF: 0.0722

GnomAD4 exome AF: 0.0357 AC: 2619 AN: 73308 Hom.: 148 Cov.: 0 AF XY: 0.0370 AC XY: 1394 AN XY: 37652

Gnomad4 AFR exome AF: 0.215

Gnomad4 AMR exome AF: 0.0238

Gnomad4 ASJ exome AF: 0.0215

Gnomad4 EAS exome AF: 0.119

Gnomad4 SAS exome AF: 0.0918

Gnomad4 FIN exome AF: 0.00139

Gnomad4 NFE exome AF: 0.0147

Gnomad4 OTH exome AF: 0.0362

GnomAD4 genome AF: 0.0859 AC: 13076 AN: 152168 Hom.: 1332 Cov.: 32 AF XY: 0.0837 AC XY: 6229 AN XY: 74394

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.0341

Gnomad4 ASJ AF: 0.0271

Gnomad4 EAS AF: 0.139

Gnomad4 SAS AF: 0.126

Gnomad4 FIN AF: 0.00179

Gnomad4 NFE AF: 0.0178

Gnomad4 OTH AF: 0.0752

Alfa AF: 0.0266 Hom.: 212

Bravo AF: 0.0937

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	5.3
Dann	Benign	0.77

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: rs10201627; hg19: chr2-231774377;