rs9296344
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001955.5(EDN1):c.*728T>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 0.142 in 152,238 control chromosomes in the GnomAD database, including 2,991 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 0.14 ( 2990 hom., cov: 32)
Exomes 𝑓: 0.10 ( 1 hom. )
Consequence
EDN1
NM_001955.5 3_prime_UTR
NM_001955.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.850
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]
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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=-0.85).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EDN1 | NM_001955.5 | c.*728T>C | 3_prime_UTR_variant | 5/5 | ENST00000379375.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EDN1 | ENST00000379375.6 | c.*728T>C | 3_prime_UTR_variant | 5/5 | 1 | NM_001955.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.142 AC: 21547AN: 151986Hom.: 2979 Cov.: 32
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GnomAD4 exome AF: 0.104 AC: 14AN: 134Hom.: 1 Cov.: 0 AF XY: 0.0962 AC XY: 5AN XY: 52
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GnomAD4 genome ? AF: 0.142 AC: 21581AN: 152104Hom.: 2990 Cov.: 32 AF XY: 0.137 AC XY: 10206AN XY: 74374
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at