chr3-68977760-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001278689.2(EOGT):c.1442A>G(p.His481Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000292 in 1,609,442 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 (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H481Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_001278689.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EOGT | NM_001278689.2 | c.1442A>G | p.His481Arg | missense_variant | 18/18 | ENST00000383701.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EOGT | ENST00000383701.8 | c.1442A>G | p.His481Arg | missense_variant | 18/18 | 1 | NM_001278689.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152200Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000854 AC: 21AN: 246008Hom.: 0 AF XY: 0.000128 AC XY: 17AN XY: 133158
GnomAD4 exome AF: 0.0000302 AC: 44AN: 1457124Hom.: 0 Cov.: 31 AF XY: 0.0000511 AC XY: 37AN XY: 724766
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152318Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74492
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 05, 2022 | The c.1190A>G (p.H397R) alteration is located in exon 15 (coding exon 12) of the EOGT gene. This alteration results from a A to G substitution at nucleotide position 1190, causing the histidine (H) at amino acid position 397 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Adams-Oliver syndrome 4 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jun 10, 2022 | This sequence change replaces histidine, which is basic and polar, with arginine, which is basic and polar, at codon 397 of the EOGT protein (p.His397Arg). This variant is present in population databases (rs527256891, gnomAD 0.07%). This variant has not been reported in the literature in individuals affected with EOGT-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at