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GeneBe

rs1049353

chr6-88143916-C-Achr6-88143916-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 1P and 3B. PM2_SupportingBP4_ModerateBP7

The NM_016083(CNR1):c.1359G>T(p.Thr453=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD Genomes project. 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)

Consequence

CNR1
NM_016083 synonymous

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.884

Links

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
?
Very rare variant; Number of alleles below threshold, Median coverage is 32.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.46).
BP7
?
Synonymous conserved (PhyloP=-0.884 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CNR1NM_016083.6 linkuse as main transcriptc.1359G>T p.Thr453= synonymous_variant 2/2 ENST00000369501.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CNR1ENST00000369501.3 linkuse as main transcriptc.1359G>T p.Thr453= synonymous_variant 2/21 NM_016083.6 P1P21554-1

Frequencies

GnomAD3 genomes
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.46
Cadd
Benign
0.27
Dann
Benign
0.77

Splicing

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: rs1049353; hg19: chr6-88853635;