rs4963842

Positions:

• chr12-22683118-G-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ETNK1	NM_018638.5	c.946-1365G>T		intron_variant		ENST00000266517.9
ETNK1	XM_017019580.2	c.*4784G>T		3_prime_UTR_variant	7/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ETNK1	ENST00000266517.9	c.946-1365G>T		intron_variant		1	NM_018638.5	P1

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

Gnomad4 AFR AF: 0.165

Gnomad4 AMR AF: 0.299

Gnomad4 ASJ AF: 0.309

Gnomad4 EAS AF: 0.123

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.405

Gnomad4 NFE AF: 0.410

Gnomad4 OTH AF: 0.304

Alfa AF: 0.382 Hom.: 10907

Bravo AF: 0.296

Asia WGS AF: 0.166 AC: 577 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.25
DANN	Benign	0.45

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: rs4963842; hg19: chr12-22836052;