Variant rs2301995 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_000501.4(ELN):c.196+71G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0771 in 1,578,610 control chromosomes in the GnomAD database, including 6,167 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.11 ( 1333 hom., cov: 32)

Exomes 𝑓: 0.073 ( 4834 hom. )

Consequence

ELN
NM_000501.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.144

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BP6

Variant 7-74037810-G-A is Benign according to our data. Variant chr7-74037810-G-A is described in ClinVar as [Benign]. Clinvar id is 1297183.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.204 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ELN	NM_000501.4 linkuse as main transcript	c.196+71G>A		intron_variant		ENST00000252034.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELN	ENST00000252034.12 linkuse as main transcript	c.196+71G>A		intron_variant		1	NM_000501.4	P4	P15502-2

Frequencies

GnomAD3 genomes

AF:

0.113

AC:

17141

AN:

152064

Hom.:

1328

Cov.:

show subpopulations

Gnomad AFR

AF:

0.208

Gnomad AMI

AF:

0.0515

Gnomad AMR

AF:

0.108

Gnomad ASJ

AF:

0.0274

Gnomad EAS

AF:

0.210

Gnomad SAS

AF:

0.123

Gnomad FIN

AF:

0.0966

Gnomad MID

AF:

0.0886

Gnomad NFE

AF:

0.0563

Gnomad OTH

AF:

0.0940

GnomAD4 exome

AF:

0.0734

AC:

104631

AN:

1426428

Hom.:

4834

Cov.:

AF XY:

0.0736

AC XY:

52015

AN XY:

706824

show subpopulations

Gnomad4 AFR exome

AF:

0.220

Gnomad4 AMR exome

AF:

0.123

Gnomad4 ASJ exome

AF:

0.0320

Gnomad4 EAS exome

AF:

0.208

Gnomad4 SAS exome

AF:

0.112

Gnomad4 FIN exome

AF:

0.0863

Gnomad4 NFE exome

AF:

0.0592

Gnomad4 OTH exome

AF:

0.0848

GnomAD4 genome

AF:

0.113

AC:

17156

AN:

152182

Hom.:

1333

Cov.:

AF XY:

0.115

AC XY:

8588

AN XY:

74418

show subpopulations

Gnomad4 AFR

AF:

0.207

Gnomad4 AMR

AF:

0.108

Gnomad4 ASJ

AF:

0.0274

Gnomad4 EAS

AF:

0.210

Gnomad4 SAS

AF:

0.122

Gnomad4 FIN

AF:

0.0966

Gnomad4 NFE

AF:

0.0563

Gnomad4 OTH

AF:

0.0939

Alfa

AF:

0.0769

Hom.:

303

Bravo

AF:

0.119

Asia WGS

AF:

0.174

AC:

602

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 03, 2015	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

1.6

DANN

Benign

0.50

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