chr1-23875575-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001841.3(CNR2):c.43G>T(p.Asp15Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000515 in 1,612,034 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001841.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CNR2 | NM_001841.3 | c.43G>T | p.Asp15Tyr | missense_variant | 2/2 | ENST00000374472.5 | |
CNR2 | XM_011540629.4 | c.43G>T | p.Asp15Tyr | missense_variant | 2/2 | ||
CNR2 | XM_017000261.3 | c.43G>T | p.Asp15Tyr | missense_variant | 3/3 | ||
CNR2 | XM_047444833.1 | c.43G>T | p.Asp15Tyr | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CNR2 | ENST00000374472.5 | c.43G>T | p.Asp15Tyr | missense_variant | 2/2 | 1 | NM_001841.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152176Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000641 AC: 16AN: 249632Hom.: 0 AF XY: 0.0000814 AC XY: 11AN XY: 135090
GnomAD4 exome AF: 0.0000534 AC: 78AN: 1459740Hom.: 0 Cov.: 33 AF XY: 0.0000579 AC XY: 42AN XY: 725860
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152294Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74458
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 10, 2022 | The c.43G>T (p.D15Y) alteration is located in exon 2 (coding exon 1) of the CNR2 gene. This alteration results from a G to T substitution at nucleotide position 43, causing the aspartic acid (D) at amino acid position 15 to be replaced by a tyrosine (Y). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at