Variant rs34208922 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_000501.4(ELN):c.*501_*502insA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.30 ( 7978 hom., cov: 0)

Exomes 𝑓: 0.23 ( 3171 hom. )

Consequence

ELN
NM_000501.4 3_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:2

Conservation

PhyloP100: -0.669

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 7-74069201-C-CA is Benign according to our data. Variant chr7-74069201-C-CA is described in ClinVar as [Benign]. Clinvar id is 360671.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.487 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ELN	NM_000501.4 linkuse as main transcript	c.501_502insA		3_prime_UTR_variant	33/33	ENST00000252034.12	NP_000492.2	P15502-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ELN	ENST00000252034.12 linkuse as main transcript	c.501_502insA		3_prime_UTR_variant	33/33	1	NM_000501.4	ENSP00000252034.7		P15502-2

Frequencies

GnomAD3 genomes

AF:

0.297

AC:

45070

AN:

151896

Hom.:

7938

Cov.:

show subpopulations

Gnomad AFR

AF:

0.491

Gnomad AMI

AF:

0.271

Gnomad AMR

AF:

0.232

Gnomad ASJ

AF:

0.186

Gnomad EAS

AF:

0.0800

Gnomad SAS

AF:

0.256

Gnomad FIN

AF:

0.151

Gnomad MID

AF:

0.247

Gnomad NFE

AF:

0.242

Gnomad OTH

AF:

0.282

GnomAD4 exome

AF:

0.229

AC:

24243

AN:

105850

Hom.:

3171

Cov.:

AF XY:

0.228

AC XY:

11510

AN XY:

50420

show subpopulations

Gnomad4 AFR exome

AF:

0.485

Gnomad4 AMR exome

AF:

0.206

Gnomad4 ASJ exome

AF:

0.182

Gnomad4 EAS exome

AF:

0.101

Gnomad4 SAS exome

AF:

0.243

Gnomad4 FIN exome

AF:

0.139

Gnomad4 NFE exome

AF:

0.240

Gnomad4 OTH exome

AF:

0.252

GnomAD4 genome

AF:

0.297

AC:

45157

AN:

152014

Hom.:

7978

Cov.:

AF XY:

0.290

AC XY:

21550

AN XY:

74316

show subpopulations

Gnomad4 AFR

AF:

0.492

Gnomad4 AMR

AF:

0.232

Gnomad4 ASJ

AF:

0.186

Gnomad4 EAS

AF:

0.0799

Gnomad4 SAS

AF:

0.257

Gnomad4 FIN

AF:

0.151

Gnomad4 NFE

AF:

0.242

Gnomad4 OTH

AF:

0.278

Alfa

AF:

0.270

Hom.:

757

Bravo

AF:

0.307

Asia WGS

AF:

0.202

AC:

701

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Cutis laxa, autosomal dominant

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Supravalvar aortic stenosis

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over