rs2293337

Positions:

• chr1-204146806-C-T

Variant summary

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

The NM_018208.4(ETNK2):​c.519-42G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 1,610,302 control chromosomes in the GnomAD database, including 75,101 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 0.27 (5819 hom., cov: 33)
  • Exomes 𝑓: 0.30 (69282 hom.)
• Consequence: ETNK2 NM_018208.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.361

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=-0.59).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ETNK2	NM_018208.4	c.519-42G>A		intron_variant		ENST00000367202.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ETNK2	ENST00000367202.9	c.519-42G>A		intron_variant		1	NM_018208.4	P1

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40928 AN: 152076 Hom.: 5816 Cov.: 33

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.265

GnomAD3 exomes AF: 0.278 AC: 68409 AN: 246444 Hom.: 9803 AF XY: 0.277 AC XY: 36837 AN XY: 133040

Gnomad AFR exome AF: 0.188

Gnomad AMR exome AF: 0.275

Gnomad ASJ exome AF: 0.289

Gnomad EAS exome AF: 0.165

Gnomad SAS exome AF: 0.210

Gnomad FIN exome AF: 0.331

Gnomad NFE exome AF: 0.316

Gnomad OTH exome AF: 0.284

GnomAD4 exome AF: 0.305 AC: 444337 AN: 1458108 Hom.: 69282 Cov.: 33 AF XY: 0.302 AC XY: 218660 AN XY: 725058

Gnomad4 AFR exome AF: 0.182

Gnomad4 AMR exome AF: 0.273

Gnomad4 ASJ exome AF: 0.292

Gnomad4 EAS exome AF: 0.153

Gnomad4 SAS exome AF: 0.212

Gnomad4 FIN exome AF: 0.331

Gnomad4 NFE exome AF: 0.323

Gnomad4 OTH exome AF: 0.281

GnomAD4 genome AF: 0.269 AC: 40959 AN: 152194 Hom.: 5819 Cov.: 33 AF XY: 0.268 AC XY: 19914 AN XY: 74412

Gnomad4 AFR AF: 0.192

Gnomad4 AMR AF: 0.269

Gnomad4 ASJ AF: 0.291

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.200

Gnomad4 FIN AF: 0.334

Gnomad4 NFE AF: 0.318

Gnomad4 OTH AF: 0.268

Alfa AF: 0.304 Hom.: 3096

Bravo AF: 0.260

Asia WGS AF: 0.192 AC: 670 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	12
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: rs2293337; hg19: chr1-204115934;