7-74053320-CTGTGTG-C
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Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_000501.4(ELN):c.1096+45_1096+50del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 1,443,618 control chromosomes in the GnomAD database, including 3 homozygotes. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0050 ( 3 hom., cov: 0)
Exomes 𝑓: 0.13 ( 0 hom. )
Consequence
ELN
NM_000501.4 intron
NM_000501.4 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.33
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 -16 ACMG points.
BP6
Variant 7-74053320-CTGTGTG-C is Benign according to our data. Variant chr7-74053320-CTGTGTG-C is described in ClinVar as [Benign]. Clinvar id is 360647.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-74053320-CTGTGTG-C is described in Lovd as [Benign]. Variant chr7-74053320-CTGTGTG-C is described in Lovd as [Benign].
BA1
GnomAdExome4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ELN | NM_000501.4 | c.1096+45_1096+50del | intron_variant | ENST00000252034.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ELN | ENST00000252034.12 | c.1096+45_1096+50del | intron_variant | 1 | NM_000501.4 | P4 |
Frequencies
GnomAD3 genomes AF: 0.00502 AC: 721AN: 143600Hom.: 3 Cov.: 0
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GnomAD4 exome AF: 0.129 AC: 167807AN: 1299932Hom.: 0 AF XY: 0.131 AC XY: 84468AN XY: 646200
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GnomAD4 genome AF: 0.00504 AC: 724AN: 143686Hom.: 3 Cov.: 0 AF XY: 0.00543 AC XY: 378AN XY: 69622
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ClinVar
Significance: Benign
Submissions summary: Benign:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:2
Benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
Benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, Amsterdam University Medical Center | - | - - |
Supravalvar aortic stenosis Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 24, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Cutis laxa, autosomal dominant Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at