1-204134490-G-A

Variant names:

• chr1-204134490-G-A
• rs2293335
• NM_018208.4:c.1088+25C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001297760.2(ETNK2):​c.*9+25C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.668 in 1,609,802 control chromosomes in the GnomAD database, including 369,394 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 0.56 (26816 hom., cov: 32)
  • Exomes 𝑓: 0.68 (342578 hom.)
• Consequence: ETNK2 NM_001297760.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.87
• Publications: 8 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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001297760.2. 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.1088+25C>T		intron	N/A	NP_060678.2
	ETNK2	NM_001297760.2		c.*9+25C>T		intron	N/A	NP_001284689.1
	ETNK2	NM_001297762.2		c.965+25C>T		intron	N/A	NP_001284691.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ETNK2	ENST00000367202.9	TSL:1 MANE Select	c.1088+25C>T		intron	N/A	ENSP00000356170.4
	ETNK2	ENST00000367201.7	TSL:2	c.*9+25C>T		intron	N/A	ENSP00000356169.3
	ETNK2	ENST00000422072.5	TSL:3	c.374+25C>T		intron	N/A	ENSP00000410580.1

Frequencies

GnomAD3 genomes AF: 0.560 AC: 85042 AN: 151902 Hom.: 26795 Cov.: 32

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.766

Gnomad AMR AF: 0.679

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.710

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.697

Gnomad OTH AF: 0.595

GnomAD2 exomes AF: 0.641 AC: 158200 AN: 246648 AF XY: 0.644

Gnomad AFR exome AF: 0.225

Gnomad AMR exome AF: 0.731

Gnomad ASJ exome AF: 0.610

Gnomad EAS exome AF: 0.518

Gnomad FIN exome AF: 0.707

Gnomad NFE exome AF: 0.697

Gnomad OTH exome AF: 0.665

GnomAD4 exome AF: 0.680 AC: 990957 AN: 1457782 Hom.: 342578 Cov.: 35 AF XY: 0.677 AC XY: 491189 AN XY: 725064

African (AFR) AF: 0.217 AC: 7233 AN: 33300

American (AMR) AF: 0.725 AC: 31771 AN: 43830

Ashkenazi Jewish (ASJ) AF: 0.608 AC: 15798 AN: 26002

East Asian (EAS) AF: 0.512 AC: 20297 AN: 39638

South Asian (SAS) AF: 0.589 AC: 50544 AN: 85868

European-Finnish (FIN) AF: 0.710 AC: 37831 AN: 53278

Middle Eastern (MID) AF: 0.581 AC: 3323 AN: 5716

European-Non Finnish (NFE) AF: 0.707 AC: 784741 AN: 1109926

Other (OTH) AF: 0.655 AC: 39419 AN: 60224

GnomAD4 genome AF: 0.560 AC: 85086 AN: 152020 Hom.: 26816 Cov.: 32 AF XY: 0.563 AC XY: 41794 AN XY: 74292

African (AFR) AF: 0.242 AC: 10047 AN: 41434

American (AMR) AF: 0.679 AC: 10369 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.593 AC: 2058 AN: 3470

East Asian (EAS) AF: 0.524 AC: 2704 AN: 5160

South Asian (SAS) AF: 0.594 AC: 2862 AN: 4820

European-Finnish (FIN) AF: 0.710 AC: 7514 AN: 10582

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.697 AC: 47410 AN: 67972

Other (OTH) AF: 0.596 AC: 1255 AN: 2106

Alfa AF: 0.652 Hom.: 99254

Bravo AF: 0.544

Asia WGS AF: 0.571 AC: 1988 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.012
DANN	Benign	0.68
PhyloP100		-3.9
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: rs2293335; hg19: chr1-204103618; COSMIC: COSV65819678; COSMIC: COSV65819678;