X-38352757-A-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_000531.6(OTC):c.61A>G(p.Met21Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000025 in 1,201,702 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M21T) has been classified as Uncertain significance.
Frequency
Consequence
NM_000531.6 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OTC | NM_000531.6 | c.61A>G | p.Met21Val | missense_variant | 1/10 | ENST00000039007.5 | |
OTC | NM_001407092.1 | c.61A>G | p.Met21Val | missense_variant | 3/12 | ||
OTC | XM_017029556.2 | c.61A>G | p.Met21Val | missense_variant | 1/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OTC | ENST00000039007.5 | c.61A>G | p.Met21Val | missense_variant | 1/10 | 1 | NM_000531.6 | P1 | |
OTC | ENST00000488812.1 | n.153A>G | non_coding_transcript_exon_variant | 1/6 | 5 | ||||
OTC | ENST00000643344.1 | c.61A>G | p.Met21Val | missense_variant, NMD_transcript_variant | 1/11 |
Frequencies
GnomAD3 genomes ? AF: 0.00000891 AC: 1AN: 112189Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34371
GnomAD3 exomes AF: 0.0000109 AC: 2AN: 183013Hom.: 0 AF XY: 0.0000148 AC XY: 1AN XY: 67551
GnomAD4 exome AF: 0.00000184 AC: 2AN: 1089513Hom.: 0 Cov.: 27 AF XY: 0.00000563 AC XY: 2AN XY: 355151
GnomAD4 genome ? AF: 0.00000891 AC: 1AN: 112189Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34371
ClinVar
Submissions by phenotype
Ornithine carbamoyltransferase deficiency Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | May 21, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at