19-54155378-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM1PM2
The NM_014516.4(CNOT3):c.2233C>T(p.Arg745Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014516.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CNOT3 | NM_014516.4 | c.2233C>T | p.Arg745Cys | missense_variant | Exon 18 of 18 | ENST00000221232.11 | NP_055331.1 | |
LENG1 | NM_024316.3 | c.*343G>A | 3_prime_UTR_variant | Exon 4 of 4 | ENST00000222224.4 | NP_077292.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CNOT3 | ENST00000221232.11 | c.2233C>T | p.Arg745Cys | missense_variant | Exon 18 of 18 | 1 | NM_014516.4 | ENSP00000221232.5 | ||
LENG1 | ENST00000222224 | c.*343G>A | 3_prime_UTR_variant | Exon 4 of 4 | 1 | NM_024316.3 | ENSP00000222224.3 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome Cov.: 30
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not provided Uncertain:1
Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at