rs10201627

Variant names:

• chr2-230909662-C-A
• rs10201627
• ENST00000444078.5:n.*341G>T

Your query was ambiguous. Multiple possible variants found:

• chr2-230909662-C-A
• chr2-230909662-C-G
• chr2-230909662-C-T

Variant summary

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

The ENST00000444078.5(GPR55):​n.*341G>T variant causes a non coding transcript exon 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 ENST00000444078.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0580
• Publications: 5 publications found

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]

ENSG00000230385 (HGNC:40260):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000444078.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GPR55	NM_005683.4	MANE Select	c.*341G>T		3_prime_UTR	Exon 2 of 2	NP_005674.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GPR55	ENST00000444078.5	TSL:1	n.*341G>T		non_coding_transcript_exon	Exon 2 of 3	ENSP00000410267.1
	GPR55	ENST00000650999.1	MANE Select	c.*341G>T		3_prime_UTR	Exon 2 of 2	ENSP00000498258.1
	GPR55	ENST00000622008.4	TSL:1	c.*341G>T		3_prime_UTR	Exon 2 of 3	ENSP00000482381.1

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

African (AFR) AF: 0.215 AC: 540 AN: 2508

American (AMR) AF: 0.0238 AC: 108 AN: 4532

Ashkenazi Jewish (ASJ) AF: 0.0215 AC: 48 AN: 2230

East Asian (EAS) AF: 0.119 AC: 605 AN: 5096

South Asian (SAS) AF: 0.0918 AC: 474 AN: 5164

European-Finnish (FIN) AF: 0.00139 AC: 4 AN: 2878

Middle Eastern (MID) AF: 0.0294 AC: 9 AN: 306

European-Non Finnish (NFE) AF: 0.0147 AC: 681 AN: 46454

Other (OTH) AF: 0.0362 AC: 150 AN: 4140

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

African (AFR) AF: 0.234 AC: 9723 AN: 41468

American (AMR) AF: 0.0341 AC: 521 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0271 AC: 94 AN: 3466

East Asian (EAS) AF: 0.139 AC: 720 AN: 5178

South Asian (SAS) AF: 0.126 AC: 609 AN: 4818

European-Finnish (FIN) AF: 0.00179 AC: 19 AN: 10610

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0178 AC: 1210 AN: 68020

Other (OTH) AF: 0.0752 AC: 159 AN: 2114

Alfa AF: 0.0354 Hom.: 451

Bravo AF: 0.0937

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.3
DANN	Benign	0.77
PhyloP100		0.058
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: rs10201627; hg19: chr2-231774377;