Variant chr1-23874772-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001841.3(CNR2):c.846T>C(p.Ala282=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.594 in 1,613,860 control chromosomes in the GnomAD database, including 287,075 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 0.63 ( 31020 hom., cov: 32)

Exomes 𝑓: 0.59 ( 256055 hom. )

Consequence

CNR2
NM_001841.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.431

Variant links:

Genes affected

CNR2 (HGNC:2160): (cannabinoid receptor 2) The cannabinoid delta-9-tetrahydrocannabinol is the principal psychoactive ingredient of marijuana. The proteins encoded by this gene and the cannabinoid receptor 1 (brain) (CNR1) gene have the characteristics of a guanine nucleotide-binding protein (G-protein)-coupled receptor for cannabinoids. They inhibit adenylate cyclase activity in a dose-dependent, stereoselective, and pertussis toxin-sensitive manner. These proteins have been found to be involved in the cannabinoid-induced CNS effects (including alterations in mood and cognition) experienced by users of marijuana. The cannabinoid receptors are members of family 1 of the G-protein-coupled receptors. [provided by RefSeq, Jul 2008]

CNR2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.67).

BP7

Synonymous conserved (PhyloP=0.431 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.749 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
CNR2	NM_001841.3 linkuse as main transcript	c.846T>C	p.Ala282=	synonymous_variant	2/2	ENST00000374472.5	NP_001832.1
CNR2	XM_011540629.4 linkuse as main transcript	c.846T>C	p.Ala282=	synonymous_variant	2/2		XP_011538931.1
CNR2	XM_017000261.3 linkuse as main transcript	c.846T>C	p.Ala282=	synonymous_variant	3/3		XP_016855750.1
CNR2	XM_047444833.1 linkuse as main transcript	c.846T>C	p.Ala282=	synonymous_variant	2/2		XP_047300789.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CNR2	ENST00000374472.5 linkuse as main transcript	c.846T>C	p.Ala282=	synonymous_variant	2/2	1	NM_001841.3	ENSP00000363596	P1

Frequencies

GnomAD3 genomes

AF:

0.635

AC:

96436

AN:

151958

Hom.:

31010

Cov.:

show subpopulations

Gnomad AFR

AF:

0.757

Gnomad AMI

AF:

0.550

Gnomad AMR

AF:

0.641

Gnomad ASJ

AF:

0.581

Gnomad EAS

AF:

0.526

Gnomad SAS

AF:

0.713

Gnomad FIN

AF:

0.576

Gnomad MID

AF:

0.703

Gnomad NFE

AF:

0.574

Gnomad OTH

AF:

0.619

GnomAD3 exomes

AF:

0.617

AC:

155135

AN:

251322

Hom.:

48586

AF XY:

0.618

AC XY:

83883

AN XY:

135836

show subpopulations

Gnomad AFR exome

AF:

0.761

Gnomad AMR exome

AF:

0.686

Gnomad ASJ exome

AF:

0.575

Gnomad EAS exome

AF:

0.529

Gnomad SAS exome

AF:

0.717

Gnomad FIN exome

AF:

0.583

Gnomad NFE exome

AF:

0.574

Gnomad OTH exome

AF:

0.611

GnomAD4 exome

AF:

0.589

AC:

861510

AN:

1461784

Hom.:

256055

Cov.:

AF XY:

0.593

AC XY:

431033

AN XY:

727206

show subpopulations

Gnomad4 AFR exome

AF:

0.766

Gnomad4 AMR exome

AF:

0.680

Gnomad4 ASJ exome

AF:

0.573

Gnomad4 EAS exome

AF:

0.569

Gnomad4 SAS exome

AF:

0.719

Gnomad4 FIN exome

AF:

0.574

Gnomad4 NFE exome

AF:

0.571

Gnomad4 OTH exome

AF:

0.593

GnomAD4 genome

AF:

0.634

AC:

96488

AN:

152076

Hom.:

31020

Cov.:

AF XY:

0.638

AC XY:

47402

AN XY:

74352

show subpopulations

Gnomad4 AFR

AF:

0.756

Gnomad4 AMR

AF:

0.641

Gnomad4 ASJ

AF:

0.581

Gnomad4 EAS

AF:

0.525

Gnomad4 SAS

AF:

0.714

Gnomad4 FIN

AF:

0.576

Gnomad4 NFE

AF:

0.574

Gnomad4 OTH

AF:

0.613

Alfa

AF:

0.591

Hom.:

34156

Bravo

AF:

0.644

Asia WGS

AF:

0.632

AC:

2197

AN:

3478

EpiCase

AF:

0.578

EpiControl

AF:

0.591

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.67

CADD

Benign

8.6

DANN

Benign

0.69

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over