rs727503030
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 3P and 4B. PVS1_ModeratePP5BS2
The NM_000501.4(ELN):c.1150+1G>A variant causes a splice donor change. The variant allele was found at a frequency of 0.000115 in 1,613,994 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000501.4 splice_donor
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ELN | NM_000501.4 | c.1150+1G>A | splice_donor_variant | ENST00000252034.12 | NP_000492.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ELN | ENST00000252034.12 | c.1150+1G>A | splice_donor_variant | 1 | NM_000501.4 | ENSP00000252034 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0000525 AC: 8AN: 152242Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000596 AC: 15AN: 251494Hom.: 0 AF XY: 0.0000441 AC XY: 6AN XY: 135920
GnomAD4 exome AF: 0.000122 AC: 178AN: 1461752Hom.: 0 Cov.: 32 AF XY: 0.000128 AC XY: 93AN XY: 727170
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152242Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74376
ClinVar
Submissions by phenotype
Supravalvar aortic stenosis Pathogenic:3
Pathogenic, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Sep 21, 2016 | The c.1150+1G>A variant in ELN has not been reported in the literature but has b een previously identified by our laboratory in 1 individual with mid-thoracic sy ndrome. This variant has been identified in 6/66734 European chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org). Please not e that for diseases with clinical variability, reduced penetrance, or recessive inheritance, pathogenic variants may be present at a low frequency in the genera l population. This variant occurs in the invariant region (+/- 1,2) of the splic e consensus sequence and is predicted to cause altered splicing leading to an ab normal or absent protein. Splice-site alterations and other loss-of-function var iants in the ELN gene are established as disease-causing for supravalvular aorti c stenosis (SVAS; Human Gene Mutation Database, HGMD). In summary, this variant meets our criteria to be classified as pathogenic for SVAS in an autosomal domin ant manner based on the predicted impact of the variant. - |
Likely pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 30, 2023 | This sequence change affects a donor splice site in intron 19 of the ELN gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in ELN are known to be pathogenic (PMID: 11175284). This variant is present in population databases (rs727503030, gnomAD 0.01%). Disruption of this splice site has been observed in individual(s) with clinical features of ELN-related conditions (PMID: 29555671, 29907982). ClinVar contains an entry for this variant (Variation ID: 163391). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. - |
Likely pathogenic, criteria provided, single submitter | clinical testing | Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine | Aug 13, 2019 | The c.1150+1G>A variant in ELN occurs in the canonical splice donor site in intron 19 and is predicted to cause altered splicing and abnormal or absent protein. While this particular variant has not been reported in the literature, other loss-of-function variants in ELN are considered disease-causing for supravalvular aortic stenosis (SVAS) (PMID: 9215670, 11175284). This variant has been seen in 17/282874 alleles in the Genome Aggregation Database (gnomAD), however ELN-associated SVAS can occur as an autosomal dominant condition with reduced penetrance (PMID: 11175284). This variant is thus considered likely pathogenic. - |
not provided Uncertain:3
Uncertain significance, criteria provided, single submitter | clinical testing | AiLife Diagnostics, AiLife Diagnostics | Dec 10, 2021 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Sep 02, 2022 | Identified in one individual with TAAD in published literature (Overwater et al., 2018); Identified as a variant of uncertain significance in an individual with a congenital heart defect who also harbored a variant in the TEAD2 gene, which was thought to be a plausible explanation for the phenotype (Szot et al., 2018); Canonical splice site variant with an unclear effect on protein function; This variant is associated with the following publications: (PMID: 31589614, 29555671, 29907982) - |
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2024 | ELN: PP3 - |
Supravalvar aortic stenosis;C3276539:Cutis laxa, autosomal dominant 1 Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Jan 26, 2018 | - - |
Hypertelorism;C1851712:Dural ectasia;C2937220:Venous malformation;C3550704:Abnormal digit morphology Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Centre for Mendelian Genomics, University Medical Centre Ljubljana | Jan 01, 2017 | - - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Mendelics | May 04, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at