Variant rs3914188 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001100121.2(ECE2):c.*22G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.731 in 1,611,682 control chromosomes in the GnomAD database, including 432,121 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 0.73 ( 40981 hom., cov: 33)

Exomes 𝑓: 0.73 ( 391140 hom. )

Consequence

ECE2
NM_001100121.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.70

Variant links:

Genes affected

ECE2 (HGNC:13275): (endothelin converting enzyme 2) Enables metalloendopeptidase activity. Involved in peptide hormone processing. Located in cytoplasmic vesicle membrane. [provided by Alliance of Genome Resources, Apr 2022]

ECE2 links:

EEF1AKMT4-ECE2 (HGNC:53615): (EEF1AKMT4-ECE2 readthrough) This gene represents naturally occurring readthrough transcription between adjacent genes eukaryotic translation elongation factor 1 alpha lysine methyltransferase 4 (GeneID: 110599564) and endothelin converting enzyme 2 (GeneID:9718). The readthrough transcript representing this gene encodes a fusion protein that shares sequence identity with each individual gene product. [provided by RefSeq, Jul 2017]

EEF1AKMT4-ECE2 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=-0.84).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.776 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein	UniProt
ECE2	NM_001100121.2 linkuse as main transcript	c.*22G>C	3_prime_UTR_variant	19/19	ENST00000404464.8	NP_001093591.1	P0DPD6-2P0DPD8
EEF1AKMT4-ECE2	NM_014693.4 linkuse as main transcript	c.*22G>C	3_prime_UTR_variant	19/19		NP_055508.3	P0DPD6P0DPD8-1
ECE2	NM_001100120.2 linkuse as main transcript	c.*22G>C	3_prime_UTR_variant	19/19		NP_001093590.1	P0DPD6-4P0DPD8
ECE2	NM_001037324.3 linkuse as main transcript	c.*22G>C	3_prime_UTR_variant	18/18		NP_001032401.1	P0DPD6-3P0DPD8

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	UniProt
ECE2	ENST00000404464.8 linkuse as main transcript	c.*22G>C	3_prime_UTR_variant	19/19	1	NM_001100121.2	ENSP00000385846.3	P0DPD6-2
EEF1AKMT4-ECE2	ENST00000402825.7 linkuse as main transcript	c.*22G>C	3_prime_UTR_variant	19/19	1		ENSP00000384223.3	P0DPD8-1
ECE2	ENST00000357474.9 linkuse as main transcript	c.*22G>C	3_prime_UTR_variant	19/19	1		ENSP00000350066.5	P0DPD6-4
ECE2	ENST00000359140.8 linkuse as main transcript	c.*22G>C	3_prime_UTR_variant	18/18	1		ENSP00000352052.4	P0DPD6-3

Frequencies

GnomAD3 genomes

AF:

0.733

AC:

111366

AN:

152022

Hom.:

40957

Cov.:

show subpopulations

Gnomad AFR

AF:

0.740

Gnomad AMI

AF:

0.663

Gnomad AMR

AF:

0.787

Gnomad ASJ

AF:

0.832

Gnomad EAS

AF:

0.623

Gnomad SAS

AF:

0.674

Gnomad FIN

AF:

0.666

Gnomad MID

AF:

0.851

Gnomad NFE

AF:

0.733

Gnomad OTH

AF:

0.769

GnomAD3 exomes

AF:

0.734

AC:

182827

AN:

249142

Hom.:

67583

AF XY:

0.730

AC XY:

98573

AN XY:

134994

show subpopulations

Gnomad AFR exome

AF:

0.736

Gnomad AMR exome

AF:

0.816

Gnomad ASJ exome

AF:

0.835

Gnomad EAS exome

AF:

0.634

Gnomad SAS exome

AF:

0.688

Gnomad FIN exome

AF:

0.670

Gnomad NFE exome

AF:

0.739

Gnomad OTH exome

AF:

0.749

GnomAD4 exome

AF:

0.731

AC:

1067083

AN:

1459544

Hom.:

391140

Cov.:

AF XY:

0.730

AC XY:

529529

AN XY:

725820

show subpopulations

Gnomad4 AFR exome

AF:

0.734

Gnomad4 AMR exome

AF:

0.812

Gnomad4 ASJ exome

AF:

0.836

Gnomad4 EAS exome

AF:

0.629

Gnomad4 SAS exome

AF:

0.685

Gnomad4 FIN exome

AF:

0.675

Gnomad4 NFE exome

AF:

0.734

Gnomad4 OTH exome

AF:

0.743

GnomAD4 genome

AF:

0.732

AC:

111436

AN:

152138

Hom.:

40981

Cov.:

AF XY:

0.727

AC XY:

54104

AN XY:

74390

show subpopulations

Gnomad4 AFR

AF:

0.740

Gnomad4 AMR

AF:

0.787

Gnomad4 ASJ

AF:

0.832

Gnomad4 EAS

AF:

0.623

Gnomad4 SAS

AF:

0.675

Gnomad4 FIN

AF:

0.666

Gnomad4 NFE

AF:

0.733

Gnomad4 OTH

AF:

0.760

Alfa

AF:

0.757

Hom.:

6741

Bravo

AF:

0.746

Asia WGS

AF:

0.653

AC:

2275

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

8.7

DANN

Benign

0.64

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