rs3914188

chr3-184292260-G-C

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.70

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]

EEF1AKMT4-ECE2 (HGNC:):

ACMG classification

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	HGVSp	Effect	#exon/exons	MANE	UniProt
ECE2	NM_001100121.2	c.*22G>C		3_prime_UTR_variant	19/19	ENST00000404464.8
EEF1AKMT4-ECE2	NM_014693.4	c.*22G>C		3_prime_UTR_variant	19/19
ECE2	NM_001037324.3	c.*22G>C		3_prime_UTR_variant	18/18
ECE2	NM_001100120.2	c.*22G>C		3_prime_UTR_variant	19/19

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ECE2	ENST00000404464.8	c.*22G>C		3_prime_UTR_variant	19/19	1	NM_001100121.2	P1
ECE2	ENST00000357474.9	c.*22G>C		3_prime_UTR_variant	19/19	1
ECE2	ENST00000359140.8	c.*22G>C		3_prime_UTR_variant	18/18	1

Frequencies

GnomAD3 genomes AF: 0.733 AC: 111366 AN: 152022 Hom.: 40957 Cov.: 33

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

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.: 47 AF XY: 0.730 AC XY: 529529 AN XY: 725820

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.: 33 AF XY: 0.727 AC XY: 54104 AN XY: 74390

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

Other links and lift over

dbSNP: rs3914188; hg19: chr3-184010048; COSMIC: COSV62569017; COSMIC: COSV62569017;