X-38412010-A-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_000531.6(OTC):c.1005+11A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000063 in 1,207,023 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 24 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000531.6 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OTC | ENST00000039007.5 | c.1005+11A>T | intron_variant | Intron 9 of 9 | 1 | NM_000531.6 | ENSP00000039007.4 | |||
ENSG00000250349 | ENST00000465127.1 | c.172-254111A>T | intron_variant | Intron 3 of 8 | 5 | ENSP00000417050.1 | ||||
OTC | ENST00000643344.1 | n.*755+11A>T | intron_variant | Intron 10 of 10 | ENSP00000496606.1 |
Frequencies
GnomAD3 genomes AF: 0.0000445 AC: 5AN: 112279Hom.: 0 Cov.: 23 AF XY: 0.0000290 AC XY: 1AN XY: 34427
GnomAD3 exomes AF: 0.0000983 AC: 18AN: 183143Hom.: 0 AF XY: 0.0000887 AC XY: 6AN XY: 67659
GnomAD4 exome AF: 0.0000649 AC: 71AN: 1094744Hom.: 0 Cov.: 29 AF XY: 0.0000639 AC XY: 23AN XY: 360214
GnomAD4 genome AF: 0.0000445 AC: 5AN: 112279Hom.: 0 Cov.: 23 AF XY: 0.0000290 AC XY: 1AN XY: 34427
ClinVar
Submissions by phenotype
Ornithine carbamoyltransferase deficiency Uncertain:1Benign:1
This variant was classified as: Uncertain significance. The available evidence on this variant's pathogenicity is insufficient or conflicting. The following ACMG criteria were applied in classifying this variant: BS2. -
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Global developmental delay;C5574662:Hyperammonemia Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at