rs4963842

Variant names:

• chr12-22683118-G-T
• rs4963842
• NM_018638.5:c.946-1365G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018638.5(ETNK1):​c.946-1365G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 152,014 control chromosomes in the GnomAD database, including 8,320 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 0.31 (8320 hom., cov: 32)
• Consequence: ETNK1 NM_018638.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.786
• Publications: 4 publications found

Genes affected

ETNK1 (HGNC:24649): (ethanolamine kinase 1) This gene encodes an ethanolamine kinase, which functions in the first committed step of the phosphatidylethanolamine synthesis pathway. This cytosolic enzyme is specific for ethanolamine and exhibits negligible kinase activity on choline. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.406 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018638.5. 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
	ETNK1	NM_018638.5	MANE Select	c.946-1365G>T		intron	N/A	NP_061108.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ETNK1	ENST00000266517.9	TSL:1 MANE Select	c.946-1365G>T		intron	N/A	ENSP00000266517.4
	ETNK1	ENST00000538218.2	TSL:1	c.1004+779G>T		intron	N/A	ENSP00000446292.2
	ETNK1	ENST00000671733.1		c.1213-1365G>T		intron	N/A	ENSP00000500633.1

Frequencies

GnomAD3 genomes AF: 0.311 AC: 47296 AN: 151896 Hom.: 8313 Cov.: 32

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.311 AC: 47324 AN: 152014 Hom.: 8320 Cov.: 32 AF XY: 0.309 AC XY: 22940 AN XY: 74274

African (AFR) AF: 0.165 AC: 6840 AN: 41478

American (AMR) AF: 0.299 AC: 4556 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.309 AC: 1070 AN: 3468

East Asian (EAS) AF: 0.123 AC: 637 AN: 5178

South Asian (SAS) AF: 0.239 AC: 1152 AN: 4826

European-Finnish (FIN) AF: 0.405 AC: 4275 AN: 10544

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.410 AC: 27858 AN: 67950

Other (OTH) AF: 0.304 AC: 643 AN: 2114

Alfa AF: 0.370 Hom.: 13409

Bravo AF: 0.296

Asia WGS AF: 0.166 AC: 577 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.25
DANN	Benign	0.45
PhyloP100		-0.79
Mutation Taster		=100/0	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: rs4963842; hg19: chr12-22836052;