rs2293337
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_018208.4(ETNK2):c.519-42G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 1,610,302 control chromosomes in the GnomAD database, including 75,101 homozygotes. 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 0.27 ( 5819 hom., cov: 33)
Exomes 𝑓: 0.30 ( 69282 hom. )
Consequence
ETNK2
NM_018208.4 intron
NM_018208.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.361
Genes affected
ETNK2 (HGNC:25575): (ethanolamine kinase 2) The protein encoded by this gene is a member of choline/ethanolamine kinase family which catalyzes the first step of phosphatidylethanolamine (PtdEtn) biosynthesis via the cytidine diphosphate (CDP) ethanolamine pathway. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.59).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ETNK2 | NM_018208.4 | c.519-42G>A | intron_variant | ENST00000367202.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ETNK2 | ENST00000367202.9 | c.519-42G>A | intron_variant | 1 | NM_018208.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.269 AC: 40928AN: 152076Hom.: 5816 Cov.: 33
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GnomAD3 exomes AF: 0.278 AC: 68409AN: 246444Hom.: 9803 AF XY: 0.277 AC XY: 36837AN XY: 133040
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GnomAD4 exome AF: 0.305 AC: 444337AN: 1458108Hom.: 69282 Cov.: 33 AF XY: 0.302 AC XY: 218660AN XY: 725058
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GnomAD4 genome ? AF: 0.269 AC: 40959AN: 152194Hom.: 5819 Cov.: 33 AF XY: 0.268 AC XY: 19914AN XY: 74412
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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