rs144884919
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001278689.2(EOGT):c.620+17G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000203 in 1,578,576 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000021 ( 0 hom. )
Consequence
EOGT
NM_001278689.2 intron
NM_001278689.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0290
Genes affected
EOGT (HGNC:28526): (EGF domain specific O-linked N-acetylglucosamine transferase) This gene encodes an enzyme that acts in the lumen of the endoplasmic reticulum to catalyze the transfer of N-acetylglucosamine to serine or threonine residues of extracellular-targeted proteins. This enzyme modifies proteins containing eukaryotic growth factor (EGF)-like domains, including the Notch receptor, thereby regulating developmental signalling. Mutations in this gene have been observed in individuals with Adams-Oliver syndrome 4. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2015]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| EOGT | NM_001278689.2 | c.620+17G>T | intron_variant | ENST00000383701.8 | NP_001265618.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| EOGT | ENST00000383701.8 | c.620+17G>T | intron_variant | 1 | NM_001278689.2 | ENSP00000373206 | P1 |
Frequencies
GnomAD3 genomes 0.0000131 AC: 2AN: 152130Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.0000122 AC: 3AN: 246276Hom.: 0 AF XY: 0.0000150 AC XY: 2AN XY: 132966
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GnomAD4 exome AF: 0.0000210 AC: 30AN: 1426328Hom.: 0 Cov.: 27 AF XY: 0.0000197 AC XY: 14AN XY: 711246
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GnomAD4 genome 0.0000131 AC: 2AN: 152248Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74452
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Not reported inComputational scores
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Benign
CADD
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DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at