rs3795578

Variant names:

• chr1-204143856-G-A
• rs3795578
• NM_018208.4:c.642-2399C>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ETNK2	NM_018208.4	c.642-2399C>T		intron_variant	Intron 3 of 7	ENST00000367202.9	NP_060678.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ETNK2	ENST00000367202.9	c.642-2399C>T		intron_variant	Intron 3 of 7	1	NM_018208.4	ENSP00000356170.4

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

African (AFR) AF: 0.332 AC: 13734 AN: 41356

American (AMR) AF: 0.378 AC: 5776 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 1379 AN: 3466

East Asian (EAS) AF: 0.408 AC: 2098 AN: 5138

South Asian (SAS) AF: 0.447 AC: 2150 AN: 4808

European-Finnish (FIN) AF: 0.456 AC: 4796 AN: 10516

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.475 AC: 32281 AN: 67946

Other (OTH) AF: 0.399 AC: 842 AN: 2108

Alfa AF: 0.451 Hom.: 66126

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
PhyloP100		0.11
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3795578; hg19: chr1-204112984;