rs28763986
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000501.4(ELN):c.1414+24C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.564 in 1,611,374 control chromosomes in the GnomAD database, including 259,425 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.60 ( 28146 hom., cov: 31)
Exomes 𝑓: 0.56 ( 231279 hom. )
Consequence
ELN
NM_000501.4 intron
NM_000501.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.37
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
?
Variant 7-74057720-C-T is Benign according to our data. Variant chr7-74057720-C-T is described in ClinVar as [Benign]. Clinvar id is 1249499.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.687 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ELN | NM_000501.4 | c.1414+24C>T | intron_variant | ENST00000252034.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ELN | ENST00000252034.12 | c.1414+24C>T | intron_variant | 1 | NM_000501.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.604 AC: 91768AN: 151840Hom.: 28115 Cov.: 31
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GnomAD3 exomes AF: 0.590 AC: 147337AN: 249772Hom.: 44055 AF XY: 0.592 AC XY: 80147AN XY: 135280
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GnomAD4 exome AF: 0.560 AC: 817610AN: 1459414Hom.: 231279 Cov.: 43 AF XY: 0.564 AC XY: 409615AN XY: 726036
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GnomAD4 genome ? AF: 0.604 AC: 91837AN: 151960Hom.: 28146 Cov.: 31 AF XY: 0.609 AC XY: 45210AN XY: 74268
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Cutis laxa, autosomal dominant 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 30, 2021 | - - |
Computational scores
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Name
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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