rs4707436

Variant names:

• chr6-88142032-G-A
• rs4707436
• NM_016083.6:c.*1824C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-88142032-G-A
• chr6-88142032-G-T

Variant summary

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

The NM_016083.6(CNR1):​c.*1824C>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 0.3 in 152,100 control chromosomes in the GnomAD database, including 7,392 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 0.30 (7388 hom., cov: 32)
  • Exomes 𝑓: 0.29 (4 hom.)
• Consequence: CNR1 NM_016083.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.28

Genes affected

CNR1 (HGNC:2159): (cannabinoid receptor 1) This gene encodes one of two cannabinoid receptors. The cannabinoids, principally delta-9-tetrahydrocannabinol and synthetic analogs, are psychoactive ingredients of marijuana. The cannabinoid receptors are members of the guanine-nucleotide-binding protein (G-protein) coupled receptor family, which inhibit adenylate cyclase activity in a dose-dependent, stereoselective and pertussis toxin-sensitive manner. The two receptors have been found to be involved in the cannabinoid-induced CNS effects (including alterations in mood and cognition) experienced by users of marijuana. Multiple transcript variants encoding two different protein isoforms have been described for this gene. [provided by RefSeq, May 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNR1	NM_016083.6	c.*1824C>T		3_prime_UTR_variant	Exon 2 of 2	ENST00000369501.3	NP_057167.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CNR1	ENST00000369501	c.*1824C>T		3_prime_UTR_variant	Exon 2 of 2	1	NM_016083.6	ENSP00000358513.2

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45533 AN: 151826 Hom.: 7395 Cov.: 32

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.0775

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.247

GnomAD4 exome AF: 0.295 AC: 46 AN: 156 Hom.: 4 Cov.: 0 AF XY: 0.291 AC XY: 25 AN XY: 86

Gnomad4 EAS exome AF: 0.287

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.333

GnomAD4 genome AF: 0.300 AC: 45543 AN: 151944 Hom.: 7388 Cov.: 32 AF XY: 0.295 AC XY: 21895 AN XY: 74270

Gnomad4 AFR AF: 0.414

Gnomad4 AMR AF: 0.219

Gnomad4 ASJ AF: 0.198

Gnomad4 EAS AF: 0.0775

Gnomad4 SAS AF: 0.175

Gnomad4 FIN AF: 0.311

Gnomad4 NFE AF: 0.280

Gnomad4 OTH AF: 0.242

Alfa AF: 0.274 Hom.: 6009

Bravo AF: 0.297

Asia WGS AF: 0.130 AC: 452 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.1
DANN	Benign	0.56

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: rs4707436; hg19: chr6-88851751;