rs1800542
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001955.5(EDN1):c.65-46G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0543 in 1,609,308 control chromosomes in the GnomAD database, including 4,656 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.10 ( 1630 hom., cov: 33)
Exomes 𝑓: 0.049 ( 3026 hom. )
Consequence
EDN1
NM_001955.5 intron
NM_001955.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.412
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 -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
Variant 6-12292295-G-A is Benign according to our data. Variant chr6-12292295-G-A is described in ClinVar as [Benign]. Clinvar id is 1232026.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.104 AC: 15775AN: 152116Hom.: 1625 Cov.: 33
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GnomAD3 exomes AF: 0.0557 AC: 13722AN: 246412Hom.: 905 AF XY: 0.0531 AC XY: 7100AN XY: 133834
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GnomAD4 exome AF: 0.0492 AC: 71664AN: 1457074Hom.: 3026 Cov.: 32 AF XY: 0.0489 AC XY: 35489AN XY: 725098
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GnomAD4 genome AF: 0.104 AC: 15800AN: 152234Hom.: 1630 Cov.: 33 AF XY: 0.0999 AC XY: 7440AN XY: 74440
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
May 12, 2021
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at