rs1917542

Variant names:

• chr1-204145718-G-A
• rs1917542
• NM_018208.4:c.641+924C>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.641+924C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.464 in 152,054 control chromosomes in the GnomAD database, including 16,547 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 0.46 (16547 hom., cov: 32)
• Consequence: ETNK2 NM_018208.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.891
• Publications: 3 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.522 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018208.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ETNK2	NM_018208.4	MANE Select	c.641+924C>T		intron	N/A	NP_060678.2	Q9NVF9-1
	ETNK2	NM_001297760.2		c.641+924C>T		intron	N/A	NP_001284689.1	Q9NVF9-2
	ETNK2	NM_001297762.2		c.518+3985C>T		intron	N/A	NP_001284691.1	Q9NVF9-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ETNK2	ENST00000367202.9	TSL:1 MANE Select	c.641+924C>T		intron	N/A	ENSP00000356170.4	Q9NVF9-1
	ETNK2	ENST00000367201.7	TSL:2	c.641+924C>T		intron	N/A	ENSP00000356169.3	Q9NVF9-2
	ETNK2	ENST00000422699.5	TSL:3	c.239+924C>T		intron	N/A	ENSP00000405497.1	Q5SXX8

Frequencies

GnomAD3 genomes AF: 0.463 AC: 70417 AN: 151938 Hom.: 16520 Cov.: 32

Gnomad AFR AF: 0.528

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.421

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.464 AC: 70483 AN: 152054 Hom.: 16547 Cov.: 32 AF XY: 0.465 AC XY: 34599 AN XY: 74334

African (AFR) AF: 0.528 AC: 21880 AN: 41462

American (AMR) AF: 0.499 AC: 7635 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.480 AC: 1665 AN: 3468

East Asian (EAS) AF: 0.459 AC: 2369 AN: 5164

South Asian (SAS) AF: 0.477 AC: 2294 AN: 4814

European-Finnish (FIN) AF: 0.421 AC: 4458 AN: 10582

Middle Eastern (MID) AF: 0.459 AC: 133 AN: 290

European-Non Finnish (NFE) AF: 0.421 AC: 28600 AN: 67960

Other (OTH) AF: 0.479 AC: 1010 AN: 2108

Alfa AF: 0.435 Hom.: 21156

Bravo AF: 0.475

Asia WGS AF: 0.481 AC: 1667 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.50
DANN	Benign	0.49
PhyloP100		-0.89
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: rs1917542; hg19: chr1-204114846;