1-204135676-A-T

Variant names:

• chr1-204135676-A-T
• rs6679960
• NM_018208.4:c.1015-1088T>A

Variant summary

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

The NM_018208.4(ETNK2):​c.1015-1088T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 152,242 control chromosomes in the GnomAD database, including 2,045 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 (2045 hom., cov: 32)
• Consequence: ETNK2 NM_018208.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.81
• Publications: 3 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ETNK2	NM_018208.4	c.1015-1088T>A		intron_variant	Intron 6 of 7	ENST00000367202.9	NP_060678.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ETNK2	ENST00000367202.9	c.1015-1088T>A		intron_variant	Intron 6 of 7	1	NM_018208.4	ENSP00000356170.4

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22727 AN: 152124 Hom.: 2036 Cov.: 32

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.0687

Gnomad SAS AF: 0.0740

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.149 AC: 22752 AN: 152242 Hom.: 2045 Cov.: 32 AF XY: 0.147 AC XY: 10947 AN XY: 74446

African (AFR) AF: 0.247 AC: 10236 AN: 41512

American (AMR) AF: 0.127 AC: 1934 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 568 AN: 3472

East Asian (EAS) AF: 0.0683 AC: 354 AN: 5186

South Asian (SAS) AF: 0.0745 AC: 359 AN: 4822

European-Finnish (FIN) AF: 0.116 AC: 1235 AN: 10612

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7629 AN: 68030

Other (OTH) AF: 0.141 AC: 298 AN: 2116

Alfa AF: 0.0604 Hom.: 64

Bravo AF: 0.156

Asia WGS AF: 0.0880 AC: 306 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.023
DANN	Benign	0.80
PhyloP100		-3.8
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: rs6679960; hg19: chr1-204104804; COSMIC: COSV65819691; COSMIC: COSV65819691;