rs6914429

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_016083.6(CNR1):​c.-64+3806T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0994 in 152,258 control chromosomes in the GnomAD database, including 816 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 0.099 ( 816 hom., cov: 33)

Consequence

CNR1
NM_016083.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.565
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.118 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CNR1NM_016083.6 linkuse as main transcriptc.-64+3806T>G intron_variant ENST00000369501.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CNR1ENST00000369501.3 linkuse as main transcriptc.-64+3806T>G intron_variant 1 NM_016083.6 P1P21554-1
CNR1ENST00000428600.3 linkuse as main transcriptc.-64+960T>G intron_variant 1 P1P21554-1
CNR1ENST00000369499.3 linkuse as main transcriptc.-64+2260T>G intron_variant 5 P1P21554-1
CNR1ENST00000551417.2 linkuse as main transcriptc.-207+2260T>G intron_variant 5 P1P21554-1

Frequencies

GnomAD3 genomes
AF:
0.0994
AC:
15122
AN:
152140
Hom.:
816
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0902
Gnomad AMI
AF:
0.155
Gnomad AMR
AF:
0.0781
Gnomad ASJ
AF:
0.0749
Gnomad EAS
AF:
0.0167
Gnomad SAS
AF:
0.0294
Gnomad FIN
AF:
0.112
Gnomad MID
AF:
0.0316
Gnomad NFE
AF:
0.121
Gnomad OTH
AF:
0.0789
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0994
AC:
15135
AN:
152258
Hom.:
816
Cov.:
33
AF XY:
0.0968
AC XY:
7204
AN XY:
74450
show subpopulations
Gnomad4 AFR
AF:
0.0903
Gnomad4 AMR
AF:
0.0781
Gnomad4 ASJ
AF:
0.0749
Gnomad4 EAS
AF:
0.0166
Gnomad4 SAS
AF:
0.0290
Gnomad4 FIN
AF:
0.112
Gnomad4 NFE
AF:
0.121
Gnomad4 OTH
AF:
0.0781
Alfa
AF:
0.0811
Hom.:
170
Bravo
AF:
0.0949
Asia WGS
AF:
0.0300
AC:
107
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
3.6
DANN
Benign
0.81

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.

Other links and lift over

dbSNP: rs6914429; hg19: chr6-88871716; API