rs11210278
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001956.5(EDN2):c.65-98G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 1,458,372 control chromosomes in the GnomAD database, including 23,996 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 ( 2027 hom., cov: 34)
Exomes 𝑓: 0.18 ( 21969 hom. )
Consequence
EDN2
NM_001956.5 intron
NM_001956.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.19
Genes affected
EDN2 (HGNC:3177): (endothelin 2) This gene encodes a member of the endothelin protein family of secretory vasoconstrictive peptides. The preproprotein is processed to a short mature form which functions as a ligand for the endothelin receptors that initiate intracellular signaling events. This gene product is involved in a wide range of biological processes, such as hypertension and ovulation. Altered expression of this gene is implicated in tumorigenesis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2014]
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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=-0.88).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EDN2 | NM_001956.5 | c.65-98G>A | intron_variant | ENST00000372587.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EDN2 | ENST00000372587.5 | c.65-98G>A | intron_variant | 1 | NM_001956.5 | P1 | |||
EDN2 | ENST00000490783.5 | n.137-189G>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.144 AC: 21882AN: 152064Hom.: 2025 Cov.: 34
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GnomAD4 exome AF: 0.178 AC: 232128AN: 1306190Hom.: 21969 AF XY: 0.177 AC XY: 113297AN XY: 640542
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GnomAD4 genome ? AF: 0.144 AC: 21890AN: 152182Hom.: 2027 Cov.: 34 AF XY: 0.147 AC XY: 10907AN XY: 74406
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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