GeneBe

rs10579871

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_000501.4(ELN):​c.1096+27_1096+50delGTGTGTGTGTGTGTGTGTGTGTGT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000141 in 1,418,612 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 0)
Exomes 𝑓: 0.0000014 ( 0 hom. )

Consequence

ELN
NM_000501.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.33

Publications

0 publications found
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]
ELN Gene-Disease associations (from GenCC):
  • cutis laxa, autosomal dominant 1
    Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), PanelApp Australia, Ambry Genetics, Genomics England PanelApp, G2P
  • supravalvular aortic stenosis
    Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Ambry Genetics, Orphanet, Labcorp Genetics (formerly Invitae)
  • autosomal dominant cutis laxa
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
  • familial thoracic aortic aneurysm and aortic dissection
    Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000501.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
ELN
NM_000501.4
MANE Select
c.1096+27_1096+50delGTGTGTGTGTGTGTGTGTGTGTGT
intron
N/ANP_000492.2
ELN
NM_001278939.2
c.1096+27_1096+50delGTGTGTGTGTGTGTGTGTGTGTGT
intron
N/ANP_001265868.1
ELN
NM_001278915.2
c.1096+27_1096+50delGTGTGTGTGTGTGTGTGTGTGTGT
intron
N/ANP_001265844.1

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
ELN
ENST00000252034.12
TSL:1 MANE Select
c.1096+12_1096+35delTGTGTGTGTGTGTGTGTGTGTGTG
intron
N/AENSP00000252034.7
ELN
ENST00000380562.8
TSL:1
c.1096+12_1096+35delTGTGTGTGTGTGTGTGTGTGTGTG
intron
N/AENSP00000369936.4
ELN
ENST00000458204.5
TSL:1
c.1066+12_1066+35delTGTGTGTGTGTGTGTGTGTGTGTG
intron
N/AENSP00000403162.1

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD4 exome
AF:
0.00000141
AC:
2
AN:
1418612
Hom.:
0
AF XY:
0.00000284
AC XY:
2
AN XY:
703072
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
32370
American (AMR)
AF:
0.00
AC:
0
AN:
39504
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
25306
East Asian (EAS)
AF:
0.0000265
AC:
1
AN:
37718
South Asian (SAS)
AF:
0.00
AC:
0
AN:
82512
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
49146
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
4234
European-Non Finnish (NFE)
AF:
9.18e-7
AC:
1
AN:
1089286
Other (OTH)
AF:
0.00
AC:
0
AN:
58536
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.400
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
Cov.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
PhyloP100
1.3

Splicing

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

Publications

Other links and lift over

dbSNP: rs10579871; hg19: chr7-73467650; API