1-204139365-G-A

Variant names:

• chr1-204139365-G-A
• rs4951307
• NM_018208.4:c.868+670C>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.868+670C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0892 in 152,206 control chromosomes in the GnomAD database, including 676 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 0.089 (676 hom., cov: 32)
• Consequence: ETNK2 NM_018208.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.397
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.105 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ETNK2	NM_018208.4	MANE Select	c.868+670C>T		intron	N/A	NP_060678.2
	ETNK2	NM_001297760.2		c.868+670C>T		intron	N/A	NP_001284689.1
	ETNK2	NM_001297762.2		c.745+670C>T		intron	N/A	NP_001284691.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ETNK2	ENST00000367202.9	TSL:1 MANE Select	c.868+670C>T		intron	N/A	ENSP00000356170.4
	ETNK2	ENST00000367201.7	TSL:2	c.868+670C>T		intron	N/A	ENSP00000356169.3
	ETNK2	ENST00000422699.5	TSL:3	c.466+670C>T		intron	N/A	ENSP00000405497.1

Frequencies

GnomAD3 genomes AF: 0.0892 AC: 13573 AN: 152088 Hom.: 675 Cov.: 32

Gnomad AFR AF: 0.0497

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.0685

Gnomad SAS AF: 0.0717

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.0981

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

GnomAD4 genome AF: 0.0892 AC: 13574 AN: 152206 Hom.: 676 Cov.: 32 AF XY: 0.0890 AC XY: 6621 AN XY: 74406

African (AFR) AF: 0.0497 AC: 2064 AN: 41536

American (AMR) AF: 0.101 AC: 1551 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 465 AN: 3472

East Asian (EAS) AF: 0.0680 AC: 352 AN: 5174

South Asian (SAS) AF: 0.0720 AC: 347 AN: 4820

European-Finnish (FIN) AF: 0.116 AC: 1226 AN: 10586

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7289 AN: 68000

Other (OTH) AF: 0.0980 AC: 207 AN: 2112

Alfa AF: 0.101 Hom.: 1463

Bravo AF: 0.0874

Asia WGS AF: 0.0700 AC: 242 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.55
DANN	Benign	0.44
PhyloP100		-0.40
Mutation Taster		=99/1	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: rs4951307; hg19: chr1-204108493;