Genetic Variant NM_018208.4:c.519-42G>A (chr1-204146806-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.361

Publications

9 publications found

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 was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ETNK2	NM_018208.4 link	c.519-42G>A		intron_variant	Intron 2 of 7	ENST00000367202.9	NP_060678.2	Q9NVF9-1A0A024R9A8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ETNK2	ENST00000367202.9 link	c.519-42G>A		intron_variant	Intron 2 of 7	1	NM_018208.4	ENSP00000356170.4		Q9NVF9-1

Frequencies

GnomAD3 genomes

AF:

0.269

AC:

40928

AN:

152076

Hom.:

5816

Cov.:

show subpopulations

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

GnomAD2 exomes

AF:

0.278

AC:

68409

AN:

246444

AF XY:

0.277

show subpopulations

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 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.:

AF XY:

0.302

AC XY:

218660

AN XY:

725058

show subpopulations

African (AFR)

AF:

0.182

AC:

6074

AN:

33456

American (AMR)

AF:

0.273

AC:

12100

AN:

44276

Ashkenazi Jewish (ASJ)

AF:

0.292

AC:

7616

AN:

26072

East Asian (EAS)

AF:

0.153

AC:

6059

AN:

39644

South Asian (SAS)

AF:

0.212

AC:

18224

AN:

85872

European-Finnish (FIN)

AF:

0.331

AC:

17623

AN:

53252

Middle Eastern (MID)

AF:

0.236

AC:

1358

AN:

5758

European-Non Finnish (NFE)

AF:

0.323

AC:

358348

AN:

1109540

Other (OTH)

AF:

0.281

AC:

16935

AN:

60238

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.466

Heterozygous variant carriers

13954

27907

41861

55814

69768

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

11566

23132

34698

46264

57830

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.269

AC:

40959

AN:

152194

Hom.:

5819

Cov.:

AF XY:

0.268

AC XY:

19914

AN XY:

74412

show subpopulations

African (AFR)

AF:

0.192

AC:

7974

AN:

41542

American (AMR)

AF:

0.269

AC:

4113

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.291

AC:

1010

AN:

3466

East Asian (EAS)

AF:

0.158

AC:

817

AN:

5178

South Asian (SAS)

AF:

0.200

AC:

963

AN:

4826

European-Finnish (FIN)

AF:

0.334

AC:

3543

AN:

10592

Middle Eastern (MID)

AF:

0.207

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.318

AC:

21595

AN:

67982

Other (OTH)

AF:

0.268

AC:

565

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1539

3077

4616

6154

7693

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

422

844

1266

1688

2110

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.299

Hom.:

5475

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

(source)

DANN

Benign

0.80

PhyloP100

-0.36

PromoterAI

0.0092

Neutral

(source)

Mutation Taster

=99/1

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over