Variant rs1800543 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001955.5(EDN1):c.234-37T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 1,607,168 control chromosomes in the GnomAD database, including 50,182 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.24 ( 4586 hom., cov: 32)

Exomes 𝑓: 0.25 ( 45596 hom. )

Consequence

EDN1
NM_001955.5 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.354

Variant links:

Genes affected

EDN1 (HGNC:3176): (endothelin 1) This gene encodes a preproprotein that is proteolytically processed to generate a secreted peptide that belongs to the endothelin/sarafotoxin family. This peptide is a potent vasoconstrictor and its cognate receptors are therapeutic targets in the treatment of pulmonary arterial hypertension. Aberrant expression of this gene may promote tumorigenesis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2015]

EDN1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BP6

Variant 6-12293904-T-C is Benign according to our data. Variant chr6-12293904-T-C is described in ClinVar as [Benign]. Clinvar id is 1222387.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EDN1	NM_001955.5 linkuse as main transcript	c.234-37T>C		intron_variant		ENST00000379375.6	NP_001946.3	P05305Q6FH53

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EDN1	ENST00000379375.6 linkuse as main transcript	c.234-37T>C		intron_variant		1	NM_001955.5	ENSP00000368683.5		P05305

Frequencies

GnomAD3 genomes

AF:

0.243

AC:

36974

AN:

151966

Hom.:

4583

Cov.:

show subpopulations

Gnomad AFR

AF:

0.246

Gnomad AMI

AF:

0.214

Gnomad AMR

AF:

0.236

Gnomad ASJ

AF:

0.235

Gnomad EAS

AF:

0.301

Gnomad SAS

AF:

0.404

Gnomad FIN

AF:

0.218

Gnomad MID

AF:

0.206

Gnomad NFE

AF:

0.233

Gnomad OTH

AF:

0.225

GnomAD3 exomes

AF:

0.252

AC:

61922

AN:

245420

Hom.:

8474

AF XY:

0.259

AC XY:

34595

AN XY:

133380

show subpopulations

Gnomad AFR exome

AF:

0.241

Gnomad AMR exome

AF:

0.196

Gnomad ASJ exome

AF:

0.237

Gnomad EAS exome

AF:

0.291

Gnomad SAS exome

AF:

0.406

Gnomad FIN exome

AF:

0.222

Gnomad NFE exome

AF:

0.231

Gnomad OTH exome

AF:

0.238

GnomAD4 exome

AF:

0.246

AC:

357815

AN:

1455084

Hom.:

45596

Cov.:

AF XY:

0.250

AC XY:

181214

AN XY:

724128

show subpopulations

Gnomad4 AFR exome

AF:

0.244

Gnomad4 AMR exome

AF:

0.200

Gnomad4 ASJ exome

AF:

0.237

Gnomad4 EAS exome

AF:

0.289

Gnomad4 SAS exome

AF:

0.403

Gnomad4 FIN exome

AF:

0.218

Gnomad4 NFE exome

AF:

0.235

Gnomad4 OTH exome

AF:

0.255

GnomAD4 genome

AF:

0.243

AC:

36989

AN:

152084

Hom.:

4586

Cov.:

AF XY:

0.246

AC XY:

18290

AN XY:

74328

show subpopulations

Gnomad4 AFR

AF:

0.246

Gnomad4 AMR

AF:

0.236

Gnomad4 ASJ

AF:

0.235

Gnomad4 EAS

AF:

0.301

Gnomad4 SAS

AF:

0.404

Gnomad4 FIN

AF:

0.218

Gnomad4 NFE

AF:

0.233

Gnomad4 OTH

AF:

0.224

Alfa

AF:

0.237

Hom.:

1012

Bravo

AF:

0.239

Asia WGS

AF:

0.320

AC:

1112

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 11, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

4.8

DANN

Benign

0.58

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over