1-204149232-T-C

Variant names:

• chr1-204149232-T-C
• rs1997034
• NM_018208.4:c.518+471A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018208.4(ETNK2):​c.518+471A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.751 in 152,078 control chromosomes in the GnomAD database, including 42,947 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 0.75 (42947 hom., cov: 32)
• Consequence: ETNK2 NM_018208.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0380

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.76 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ETNK2	NM_018208.4	c.518+471A>G		intron_variant	Intron 2 of 7	ENST00000367202.9	NP_060678.2
ETNK2	NM_001297760.2	c.518+471A>G		intron_variant	Intron 2 of 7		NP_001284689.1
ETNK2	NM_001297762.2	c.518+471A>G		intron_variant	Intron 2 of 6		NP_001284691.1
ETNK2	NM_001297761.2	c.-17+2363A>G		intron_variant	Intron 1 of 6		NP_001284690.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ETNK2	ENST00000367202.9	c.518+471A>G		intron_variant	Intron 2 of 7	1	NM_018208.4	ENSP00000356170.4
ETNK2	ENST00000367201.7	c.518+471A>G		intron_variant	Intron 2 of 7	2		ENSP00000356169.3
ETNK2	ENST00000444817.1	c.179+471A>G		intron_variant	Intron 1 of 3	5		ENSP00000406241.1

Frequencies

GnomAD3 genomes AF: 0.750 AC: 114037 AN: 151960 Hom.: 42894 Cov.: 32

Gnomad AFR AF: 0.740

Gnomad AMI AF: 0.828

Gnomad AMR AF: 0.771

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.678

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.823

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.753

Gnomad OTH AF: 0.756

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

GnomAD4 genome AF: 0.751 AC: 114146 AN: 152078 Hom.: 42947 Cov.: 32 AF XY: 0.752 AC XY: 55897 AN XY: 74336

Gnomad4 AFR AF: 0.739

Gnomad4 AMR AF: 0.772

Gnomad4 ASJ AF: 0.732

Gnomad4 EAS AF: 0.679

Gnomad4 SAS AF: 0.669

Gnomad4 FIN AF: 0.823

Gnomad4 NFE AF: 0.753

Gnomad4 OTH AF: 0.759

Alfa AF: 0.748 Hom.: 63377

Bravo AF: 0.748

Asia WGS AF: 0.709 AC: 2461 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.8
DANN	Benign	0.59

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

Other links and lift over

dbSNP: rs1997034; hg19: chr1-204118360;