Genetic Variant ETNK2:c.642-75G>A (chr1-204141532-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_018208.4(ETNK2):c.642-75G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0979 in 1,493,010 control chromosomes in the GnomAD database, including 9,287 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 0.15 ( 2482 hom., cov: 32)

Exomes 𝑓: 0.092 ( 6805 hom. )

Consequence

ETNK2
NM_018208.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.678

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:

ERLNC1 (HGNC:41109): (estrogen receptor responsive lncRNA 1)

ERLNC1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ETNK2	NM_018208.4 link	c.642-75G>A		intron_variant	Intron 3 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.642-75G>A		intron_variant	Intron 3 of 7	1	NM_018208.4	ENSP00000356170.4		Q9NVF9-1

Frequencies

GnomAD3 genomes

AF:

0.150

AC:

22801

AN:

152076

Hom.:

2472

Cov.:

show subpopulations

Gnomad AFR

AF:

0.302

Gnomad AMI

AF:

0.0318

Gnomad AMR

AF:

0.118

Gnomad ASJ

AF:

0.153

Gnomad EAS

AF:

0.0656

Gnomad SAS

AF:

0.0967

Gnomad FIN

AF:

0.0860

Gnomad MID

AF:

0.180

Gnomad NFE

AF:

0.0862

Gnomad OTH

AF:

0.146

GnomAD4 exome

AF:

0.0920

AC:

123368

AN:

1340816

Hom.:

6805

Cov.:

AF XY:

0.0919

AC XY:

60684

AN XY:

660232

show subpopulations

Gnomad4 AFR exome

AF:

0.317

Gnomad4 AMR exome

AF:

0.117

Gnomad4 ASJ exome

AF:

0.142

Gnomad4 EAS exome

AF:

0.0575

Gnomad4 SAS exome

AF:

0.100

Gnomad4 FIN exome

AF:

0.0778

Gnomad4 NFE exome

AF:

0.0838

Gnomad4 OTH exome

AF:

0.105

GnomAD4 genome

AF:

0.150

AC:

22827

AN:

152194

Hom.:

2482

Cov.:

AF XY:

0.148

AC XY:

11041

AN XY:

74406

show subpopulations

Gnomad4 AFR

AF:

0.302

Gnomad4 AMR

AF:

0.118

Gnomad4 ASJ

AF:

0.153

Gnomad4 EAS

AF:

0.0649

Gnomad4 SAS

AF:

0.0968

Gnomad4 FIN

AF:

0.0860

Gnomad4 NFE

AF:

0.0862

Gnomad4 OTH

AF:

0.146

Alfa

AF:

0.0920

Hom.:

1115

Bravo

AF:

0.160

Asia WGS

AF:

0.101

AC:

350

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.21

DANN

Benign

0.23

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over