rs2273512
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_016083.6(CNR1):c.-64+938C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00208 in 152,190 control chromosomes in the GnomAD database, including 3 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 0.0021 ( 3 hom., cov: 33)
Consequence
CNR1
NM_016083.6 intron
NM_016083.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.208
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BS1
?
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00208 (317/152190) while in subpopulation EAS AF= 0.0349 (181/5192). AF 95% confidence interval is 0.0307. There are 3 homozygotes in gnomad4. There are 181 alleles in male gnomad4 subpopulation. This position pass quality control queck.
BS2
?
High AC in GnomAd at 314 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CNR1 | NM_016083.6 | c.-64+938C>T | intron_variant | ENST00000369501.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CNR1 | ENST00000369501.3 | c.-64+938C>T | intron_variant | 1 | NM_016083.6 | P1 | |||
CNR1 | ENST00000551417.2 | c.-244-571C>T | intron_variant | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00206 AC: 314AN: 152072Hom.: 3 Cov.: 33
GnomAD3 genomes
?
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314
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152072
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.00208 AC: 317AN: 152190Hom.: 3 Cov.: 33 AF XY: 0.00243 AC XY: 181AN XY: 74418
GnomAD4 genome
?
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317
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152190
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33
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181
AN XY:
74418
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Asia WGS
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27
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at