rs1800456
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_000274.4(OAT):c.1311G>T(p.Leu437Phe) variant causes a missense change. The variant allele was found at a frequency of 0.000776 in 1,613,670 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Benignin ClinVar. Synonymous variant affecting the same amino acid position (i.e. L437L) has been classified as Likely benign.
Frequency
Consequence
NM_000274.4 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 |
---|---|---|---|---|---|---|---|
OAT | NM_000274.4 | c.1311G>T | p.Leu437Phe | missense_variant | 10/10 | ENST00000368845.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OAT | ENST00000368845.6 | c.1311G>T | p.Leu437Phe | missense_variant | 10/10 | 1 | NM_000274.4 | P1 | |
OAT | ENST00000539214.5 | c.897G>T | p.Leu299Phe | missense_variant | 9/9 | 1 |
Frequencies
GnomAD3 genomes AF: 0.000342 AC: 52AN: 152180Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000280 AC: 70AN: 249800Hom.: 1 AF XY: 0.000288 AC XY: 39AN XY: 135386
GnomAD4 exome AF: 0.000821 AC: 1200AN: 1461490Hom.: 2 Cov.: 31 AF XY: 0.000802 AC XY: 583AN XY: 727036
GnomAD4 genome AF: 0.000342 AC: 52AN: 152180Hom.: 0 Cov.: 33 AF XY: 0.000175 AC XY: 13AN XY: 74332
ClinVar
Submissions by phenotype
Ornithine aminotransferase deficiency Pathogenic:1Benign:3
Benign, no assertion criteria provided | clinical testing | Natera, Inc. | Jan 23, 2020 | - - |
Likely pathogenic, flagged submission | literature only | Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM) | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at