rs1917542

Positions:

• chr1-204145718-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.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

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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.522 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ETNK2	NM_018208.4	c.641+924C>T		intron_variant		ENST00000367202.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ETNK2	ENST00000367202.9	c.641+924C>T		intron_variant		1	NM_018208.4	P1

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

Gnomad4 AFR AF: 0.528

Gnomad4 AMR AF: 0.499

Gnomad4 ASJ AF: 0.480

Gnomad4 EAS AF: 0.459

Gnomad4 SAS AF: 0.477

Gnomad4 FIN AF: 0.421

Gnomad4 NFE AF: 0.421

Gnomad4 OTH AF: 0.479

Alfa AF: 0.434 Hom.: 15350

Bravo AF: 0.475

Asia WGS AF: 0.481 AC: 1667 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.50
DANN	Benign	0.49

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: rs1917542; hg19: chr1-204114846;