chr7-74053320-C-CTG
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BA1
The NM_000501.4(ELN):c.1096+49_1096+50dup variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.13 ( 1264 hom., cov: 0)
Exomes 𝑓: 0.11 ( 4 hom. )
Consequence
ELN
NM_000501.4 intron
NM_000501.4 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.780
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 -9 ACMG points.
BP6
Variant 7-74053320-C-CTG is Benign according to our data. Variant chr7-74053320-C-CTG is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 360643.We mark this variant Likely_benign, oryginal submissions are: {Benign=2, Uncertain_significance=4}.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.149 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ELN | NM_000501.4 | c.1096+49_1096+50dup | intron_variant | ENST00000252034.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ELN | ENST00000252034.12 | c.1096+49_1096+50dup | intron_variant | 1 | NM_000501.4 | P4 |
Frequencies
GnomAD3 genomes AF: 0.134 AC: 19364AN: 144016Hom.: 1263 Cov.: 0
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GnomAD4 exome AF: 0.113 AC: 154927AN: 1376902Hom.: 4 Cov.: 0 AF XY: 0.112 AC XY: 76710AN XY: 682936
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GnomAD4 genome AF: 0.134 AC: 19374AN: 144118Hom.: 1264 Cov.: 0 AF XY: 0.131 AC XY: 9130AN XY: 69874
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:4Benign:2
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
Supravalvar aortic stenosis Uncertain:2Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Cutis laxa, autosomal dominant Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 26, 2019 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at