Genetic Variant NM_018208.4:c.416G>A (chr1-204149805-C-T) – ACMG Classification: Uncertain_significance (2 pts)

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_018208.4(ETNK2):c.416G>A(p.Cys139Tyr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000647 in 1,607,634 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000053 ( 0 hom., cov: 32)

Exomes 𝑓: 0.000066 ( 0 hom. )

Consequence

ETNK2
NM_018208.4 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 7.24

Variant links:

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]

ETNK2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ETNK2	NM_018208.4 link	c.416G>A	p.Cys139Tyr	missense_variant	Exon 2 of 8	ENST00000367202.9	NP_060678.2	Q9NVF9-1A0A024R9A8
ETNK2	NM_001297760.2 link	c.416G>A	p.Cys139Tyr	missense_variant	Exon 2 of 8		NP_001284689.1	Q9NVF9-2A0A024R976
ETNK2	NM_001297762.2 link	c.416G>A	p.Cys139Tyr	missense_variant	Exon 2 of 7		NP_001284691.1	Q9NVF9-3
ETNK2	NM_001297761.2 link	c.-17+1790G>A		intron_variant	Intron 1 of 6		NP_001284690.1	Q9NVF9B7Z1G7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
ETNK2	ENST00000367202.9 link	c.416G>A	p.Cys139Tyr	missense_variant	Exon 2 of 8	1	NM_018208.4	ENSP00000356170.4	Q9NVF9-1
ETNK2	ENST00000367201.7 link	c.416G>A	p.Cys139Tyr	missense_variant	Exon 2 of 8	2		ENSP00000356169.3	Q9NVF9-2
ETNK2	ENST00000444817.1 link	c.77G>A	p.Cys26Tyr	missense_variant	Exon 1 of 4	5		ENSP00000406241.1	Q5SXX7
ETNK2	ENST00000429525.1 link	c.*68G>A		downstream_gene_variant		4		ENSP00000394618.1	B7ZC35

Frequencies

GnomAD3 genomes

AF:

0.0000526

AC:

AN:

152216

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000482

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000882

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.0000209

AC:

AN:

239136

Hom.:

AF XY:

0.0000387

AC XY:

AN XY:

129228

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000465

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000660

AC:

AN:

1455418

Hom.:

Cov.:

AF XY:

0.0000622

AC XY:

AN XY:

723288

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000802

Gnomad4 OTH exome

AF:

0.000116

GnomAD4 genome

AF:

0.0000526

AC:

AN:

152216

Hom.:

Cov.:

AF XY:

0.0000672

AC XY:

AN XY:

74362

show subpopulations

Gnomad4 AFR

AF:

0.0000482

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000882

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.000116

Hom.:

Bravo

AF:

0.0000378

ExAC

AF:

0.0000247

AC:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Feb 14, 2023

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.416G>A (p.C139Y) alteration is located in exon 2 (coding exon 2) of the ETNK2 gene. This alteration results from a G to A substitution at nucleotide position 416, causing the cysteine (C) at amino acid position 139 to be replaced by a tyrosine (Y). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.75

BayesDel_addAF

Pathogenic

0.17

BayesDel_noAF

Uncertain

0.11

CADD

Pathogenic

DANN

Uncertain

0.98

DEOGEN2

Benign

0.22

.;T;.

Eigen

Uncertain

0.43

Eigen_PC

Uncertain

0.52

FATHMM_MKL

Uncertain

0.85

LIST_S2

Uncertain

0.87

D;D;D

M_CAP

Benign

0.030

MetaRNN

Uncertain

0.64

D;D;D

MetaSVM

Benign

-0.75

MutationAssessor

Benign

1.6

L;L;.

PrimateAI

Uncertain

0.68

PROVEAN

Pathogenic

-8.1

D;D;D

REVEL

Uncertain

0.38

Sift

Benign

0.15

T;T;T

Sift4G

Benign

0.12

T;T;.

Polyphen

1.0

D;P;.

Vest4

0.90

MutPred

0.59

Loss of methylation at K142 (P = 0.1458);Loss of methylation at K142 (P = 0.1458);.;

MVP

0.71

MPC

1.3

ClinPred

0.60

GERP RS

5.5

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.74

gMVP

0.92

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over