rs3795578

Positions:

• chr1-204143856-G-A
• chr1-204143856-G-T

Variant summary

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

The NM_018208.4(ETNK2):​c.642-2399C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.419 in 151,806 control chromosomes in the GnomAD database, including 13,684 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 0.42 (13684 hom., cov: 30)
• Consequence: ETNK2 NM_018208.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.112

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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.471 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ETNK2	NM_018208.4	c.642-2399C>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.642-2399C>T		intron_variant		1	NM_018208.4	ENSP00000356170	P1

Frequencies

GnomAD3 genomes AF: 0.419 AC: 63555 AN: 151688 Hom.: 13671 Cov.: 30

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.408

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.401

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.419 AC: 63593 AN: 151806 Hom.: 13684 Cov.: 30 AF XY: 0.416 AC XY: 30885 AN XY: 74160

Gnomad4 AFR AF: 0.332

Gnomad4 AMR AF: 0.378

Gnomad4 ASJ AF: 0.398

Gnomad4 EAS AF: 0.408

Gnomad4 SAS AF: 0.447

Gnomad4 FIN AF: 0.456

Gnomad4 NFE AF: 0.475

Gnomad4 OTH AF: 0.399

Alfa AF: 0.454 Hom.: 29792

Bravo AF: 0.404

Asia WGS AF: 0.405 AC: 1410 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.59
DANN	Benign	0.80

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: rs3795578; hg19: chr1-204112984;