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

Genomes: 𝑓 0.000053 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00012 ( 0 hom. )

Consequence

ELN
NM_000501.4 splice_donor

Scores

2
4
1
Splicing: ADA: 1.000
2

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:5U:4

Conservation

PhyloP100: 4.90
Variant links:
Genes affected
ELN (HGNC:3327): (elastin) This gene encodes a protein that is one of the two components of elastic fibers. Elastic fibers comprise part of the extracellular matrix and confer elasticity to organs and tissues including the heart, skin, lungs, ligaments, and blood vessels. The encoded protein is rich in hydrophobic amino acids such as glycine and proline, which form mobile hydrophobic regions bounded by crosslinks between lysine residues. Degradation products of the encoded protein, known as elastin-derived peptides or elastokines, bind the elastin receptor complex and other receptors and stimulate migration and proliferation of monocytes and skin fibroblasts. Elastokines can also contribute to cancer progression. Deletions and mutations in this gene are associated with supravalvular aortic stenosis (SVAS) and autosomal dominant cutis laxa. [provided by RefSeq, Aug 2017]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -1 ACMG points.

PVS1
Splicing +-2 bp (donor or acceptor) variant, product NOT destroyed by NMD, known LOF gene, truncates exone, which is 0.024367817 fraction of the gene. No cryptic splice site detected. Exon removal is inframe change.
PP5
Variant 7-74054770-G-A is Pathogenic according to our data. Variant chr7-74054770-G-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 163391.We mark this variant Likely_pathogenic, oryginal submissions are: {Likely_pathogenic=3, Uncertain_significance=4, Pathogenic=2}.
BS2
High AC in GnomAd4 at 8 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ELNNM_000501.4 linkuse as main transcriptc.1150+1G>A splice_donor_variant ENST00000252034.12 NP_000492.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ELNENST00000252034.12 linkuse as main transcriptc.1150+1G>A splice_donor_variant 1 NM_000501.4 ENSP00000252034 P4P15502-2

Frequencies

GnomAD3 genomes
AF:
0.0000525
AC:
8
AN:
152242
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000241
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000103
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000596
AC:
15
AN:
251494
Hom.:
0
AF XY:
0.0000441
AC XY:
6
AN XY:
135920
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.0000578
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000114
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.000122
AC:
178
AN:
1461752
Hom.:
0
Cov.:
32
AF XY:
0.000128
AC XY:
93
AN XY:
727170
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.0000447
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000156
Gnomad4 OTH exome
AF:
0.0000497
GnomAD4 genome
AF:
0.0000525
AC:
8
AN:
152242
Hom.:
0
Cov.:
32
AF XY:
0.0000403
AC XY:
3
AN XY:
74376
show subpopulations
Gnomad4 AFR
AF:
0.0000241
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000103
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000141
Hom.:
0
Bravo
AF:
0.0000604
ExAC
AF:
0.0000494
AC:
6
EpiCase
AF:
0.0000545
EpiControl
AF:
0.000119

ClinVar

Significance: Conflicting classifications of pathogenicity
Submissions summary: Pathogenic:5Uncertain:4
Revision: criteria provided, conflicting classifications
LINK: link

Submissions by phenotype

Supravalvar aortic stenosis Pathogenic:3
Pathogenic, criteria provided, single submitterclinical testingLaboratory for Molecular Medicine, Mass General Brigham Personalized MedicineSep 21, 2016The 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 submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpDec 30, 2023This 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 submitterclinical testingHuman Genome Sequencing Center Clinical Lab, Baylor College of MedicineAug 13, 2019The 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 submitterclinical testingAiLife Diagnostics, AiLife DiagnosticsDec 10, 2021- -
Uncertain significance, criteria provided, single submitterclinical testingGeneDxSep 02, 2022Identified 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 submitterclinical testingCeGaT Center for Human Genetics TuebingenJan 01, 2024ELN: PP3 -
Supravalvar aortic stenosis;C3276539:Cutis laxa, autosomal dominant 1 Pathogenic:1
Likely pathogenic, criteria provided, single submitterclinical testingMayo Clinic Laboratories, Mayo ClinicJan 26, 2018- -
Hypertelorism;C1851712:Dural ectasia;C2937220:Venous malformation;C3550704:Abnormal digit morphology Pathogenic:1
Pathogenic, criteria provided, single submitterclinical testingCentre for Mendelian Genomics, University Medical Centre LjubljanaJan 01, 2017- -
not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingMendelicsMay 04, 2022- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
0.43
D
BayesDel_noAF
Uncertain
0.040
CADD
Pathogenic
31
DANN
Uncertain
0.99
Eigen
Pathogenic
0.88
Eigen_PC
Uncertain
0.66
FATHMM_MKL
Uncertain
0.87
D
MutationTaster
Benign
1.0
D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
GERP RS
4.0

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Pathogenic
1.0
dbscSNV1_RF
Pathogenic
0.90
SpliceAI score (max)
1.0
Details are displayed if max score is > 0.2
DS_DL_spliceai
1.0
Position offset: -1

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs727503030; hg19: chr7-73469100; API