chr6-12292366-G-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_001955.5(EDN1):c.90G>T(p.Ala30=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000731 in 1,614,020 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. A30A) has been classified as Benign.
Frequency
Consequence
NM_001955.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EDN1 | NM_001955.5 | c.90G>T | p.Ala30= | synonymous_variant | 2/5 | ENST00000379375.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EDN1 | ENST00000379375.6 | c.90G>T | p.Ala30= | synonymous_variant | 2/5 | 1 | NM_001955.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000112 AC: 17AN: 152200Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000518 AC: 13AN: 251122Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135828
GnomAD4 exome AF: 0.0000691 AC: 101AN: 1461820Hom.: 2 Cov.: 32 AF XY: 0.0000798 AC XY: 58AN XY: 727220
GnomAD4 genome ? AF: 0.000112 AC: 17AN: 152200Hom.: 0 Cov.: 33 AF XY: 0.000134 AC XY: 10AN XY: 74356
ClinVar
Submissions by phenotype
EDN1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 22, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at