chr1-204134490-G-A

Position:

• chr1-204134490-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018208.4(ETNK2):​c.1088+25C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.668 in 1,609,802 control chromosomes in the GnomAD database, including 369,394 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 0.56 (26816 hom., cov: 32)
  • Exomes 𝑓: 0.68 (342578 hom.)
• Consequence: ETNK2 NM_018208.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.87

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ETNK2	NM_018208.4	c.1088+25C>T		intron_variant		ENST00000367202.9	NP_060678.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ETNK2	ENST00000367202.9	c.1088+25C>T		intron_variant		1	NM_018208.4	ENSP00000356170	P1

Frequencies

GnomAD3 genomes AF: 0.560 AC: 85042 AN: 151902 Hom.: 26795 Cov.: 32

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.766

Gnomad AMR AF: 0.679

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.710

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.697

Gnomad OTH AF: 0.595

GnomAD3 exomes AF: 0.641 AC: 158200 AN: 246648 Hom.: 52680 AF XY: 0.644 AC XY: 85930 AN XY: 133356

Gnomad AFR exome AF: 0.225

Gnomad AMR exome AF: 0.731

Gnomad ASJ exome AF: 0.610

Gnomad EAS exome AF: 0.518

Gnomad SAS exome AF: 0.592

Gnomad FIN exome AF: 0.707

Gnomad NFE exome AF: 0.697

Gnomad OTH exome AF: 0.665

GnomAD4 exome AF: 0.680 AC: 990957 AN: 1457782 Hom.: 342578 Cov.: 35 AF XY: 0.677 AC XY: 491189 AN XY: 725064

Gnomad4 AFR exome AF: 0.217

Gnomad4 AMR exome AF: 0.725

Gnomad4 ASJ exome AF: 0.608

Gnomad4 EAS exome AF: 0.512

Gnomad4 SAS exome AF: 0.589

Gnomad4 FIN exome AF: 0.710

Gnomad4 NFE exome AF: 0.707

Gnomad4 OTH exome AF: 0.655

GnomAD4 genome AF: 0.560 AC: 85086 AN: 152020 Hom.: 26816 Cov.: 32 AF XY: 0.563 AC XY: 41794 AN XY: 74292

Gnomad4 AFR AF: 0.242

Gnomad4 AMR AF: 0.679

Gnomad4 ASJ AF: 0.593

Gnomad4 EAS AF: 0.524

Gnomad4 SAS AF: 0.594

Gnomad4 FIN AF: 0.710

Gnomad4 NFE AF: 0.697

Gnomad4 OTH AF: 0.596

Alfa AF: 0.675 Hom.: 38276

Bravo AF: 0.544

Asia WGS AF: 0.571 AC: 1988 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.012
DANN	Benign	0.68

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2293335; hg19: chr1-204103618; COSMIC: COSV65819678; COSMIC: COSV65819678;