2-230909662-C-G

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000444078.5(GPR55):​n.*341G>C 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 0.0000136 in 73,340 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.000014 (0 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

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>C		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>C		non_coding_transcript_exon	Exon 2 of 3	ENSP00000410267.1
	GPR55	ENST00000650999.1	MANE Select	c.*341G>C		3_prime_UTR	Exon 2 of 2	ENSP00000498258.1
	GPR55	ENST00000622008.4	TSL:1	c.*341G>C		3_prime_UTR	Exon 2 of 3	ENSP00000482381.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.0000136 AC: 1 AN: 73340 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 37674

African (AFR) AF: 0.00 AC: 0 AN: 2514

American (AMR) AF: 0.000221 AC: 1 AN: 4534

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2232

East Asian (EAS) AF: 0.00 AC: 0 AN: 5104

South Asian (SAS) AF: 0.00 AC: 0 AN: 5168

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2878

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 306

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 46464

Other (OTH) AF: 0.00 AC: 0 AN: 4140

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 451

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.3
DANN	Benign	0.74
PhyloP100		0.058

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;