chr7-74053320-CTGTGTGTGTG-C
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2
The NM_000501.4(ELN):c.1096+41_1096+50del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00014 in 1,562,560 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.00030 ( 0 hom., cov: 0)
Exomes 𝑓: 0.00012 ( 0 hom. )
Consequence
ELN
NM_000501.4 intron
NM_000501.4 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
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 -8 ACMG points.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.000298 (43/144250) while in subpopulation AFR AF= 0.000774 (30/38764). AF 95% confidence interval is 0.000556. There are 0 homozygotes in gnomad4. There are 21 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
BS2
High AC in GnomAd4 at 43 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ELN | NM_000501.4 | c.1096+41_1096+50del | intron_variant | ENST00000252034.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ELN | ENST00000252034.12 | c.1096+41_1096+50del | intron_variant | 1 | NM_000501.4 | P4 |
Frequencies
GnomAD3 genomes AF: 0.000298 AC: 43AN: 144146Hom.: 0 Cov.: 0
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GnomAD4 exome AF: 0.000124 AC: 176AN: 1418310Hom.: 0 AF XY: 0.000124 AC XY: 87AN XY: 702902
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GnomAD4 genome AF: 0.000298 AC: 43AN: 144250Hom.: 0 Cov.: 0 AF XY: 0.000300 AC XY: 21AN XY: 69950
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ClinVar
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at