X-38352260-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001407092.1(OTC):c.-79-358T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars).
Frequency
Consequence
NM_001407092.1 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OTC | NM_001407092.1 | c.-79-358T>C | intron_variant | Intron 2 of 11 | NP_001394021.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 24
GnomAD4 genome Cov.: 24
ClinVar
Submissions by phenotype
OTC-related disorder Uncertain:1
The OTC c.-437T>C variant is located in the 5' untranslated region. To our knowledge, this variant has not been reported in the literature or in a large population database, indicating this variant is rare. Other variants in the pre-coding region of OTC have been reported in individuals with ornithine transcarbamylase deficiency but no identified sequence variant in the exon or exon/intron boundary regions of the OTC gene (Jang et al. 2018. PubMed ID: 29282796). Several of these variants were reported to reduce reported gene expression in an in vitro study (Jang et al. 2018. PubMed ID: 29282796). At this time, the clinical significance of the c.-437T>C variant is uncertain due to the absence of conclusive functional and genetic evidence. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.