NM_002539.3:c.1386G>C
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PM4
The NM_002539.3(ODC1):c.1386G>C(p.Ter462Tyrext*?) variant causes a stop lost change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,400 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002539.3 stop_lost
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 |
---|---|---|---|---|---|---|---|---|
ODC1 | NM_002539.3 | c.1386G>C | p.Ter462Tyrext*? | stop_lost | Exon 12 of 12 | ENST00000234111.9 | NP_002530.1 | |
ODC1 | NM_001287189.2 | c.1386G>C | p.Ter462Tyrext*? | stop_lost | Exon 12 of 12 | NP_001274118.1 | ||
ODC1 | NM_001287190.2 | c.1386G>C | p.Ter462Tyrext*? | stop_lost | Exon 12 of 12 | NP_001274119.1 | ||
ODC1 | NM_001287188.2 | c.999G>C | p.Ter333Tyrext*? | stop_lost | Exon 12 of 12 | NP_001274117.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461400Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 727000
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Uncertain:1
Stop codon loss and change to a tyrosine codon, leading to protein extension and the addition of 5 amino acids at the C-terminus; Not observed at significant frequency in large population cohorts (gnomAD); 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
Publications
No publications associated with this variant yet.