Variant rs10579679 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_001399.5(EDA):c.706+11_706+12del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.41 in 1,193,389 control chromosomes in the GnomAD database, including 71,235 homozygotes. There are 154,984 hemizygotes in GnomAD. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.44 ( 8117 hom., 13038 hem., cov: 0)

Exomes 𝑓: 0.41 ( 63118 hom. 141946 hem. )

Consequence

EDA
NM_001399.5 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:7

Conservation

PhyloP100: 0.988

Variant links:

Genes affected

EDA (HGNC:3157): (ectodysplasin A) The protein encoded by this gene is a type II membrane protein that can be cleaved by furin to produce a secreted form. The encoded protein, which belongs to the tumor necrosis factor family, acts as a homotrimer and may be involved in cell-cell signaling during the development of ectodermal organs. Defects in this gene are a cause of ectodermal dysplasia, anhidrotic, which is also known as X-linked hypohidrotic ectodermal dysplasia. Several transcript variants encoding many different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

EDA links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant X-70028046-CCT-C is Benign according to our data. Variant chrX-70028046-CCT-C is described in ClinVar as [Benign]. Clinvar id is 44204.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.569 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EDA	NM_001399.5 linkuse as main transcript	c.706+11_706+12del		intron_variant		ENST00000374552.9	NP_001390.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EDA	ENST00000374552.9 linkuse as main transcript	c.706+11_706+12del		intron_variant		1	NM_001399.5	ENSP00000363680	P4	Q92838-1

Frequencies

GnomAD3 genomes

AF:

0.442

AC:

47876

AN:

108293

Hom.:

8118

Cov.:

AF XY:

0.423

AC XY:

13006

AN XY:

30759

show subpopulations

Gnomad AFR

AF:

0.576

Gnomad AMI

AF:

0.390

Gnomad AMR

AF:

0.353

Gnomad ASJ

AF:

0.283

Gnomad EAS

AF:

0.176

Gnomad SAS

AF:

0.251

Gnomad FIN

AF:

0.491

Gnomad MID

AF:

0.375

Gnomad NFE

AF:

0.415

Gnomad OTH

AF:

0.404

GnomAD3 exomes

AF:

0.371

AC:

57799

AN:

155702

Hom.:

8237

AF XY:

0.356

AC XY:

17215

AN XY:

48354

show subpopulations

Gnomad AFR exome

AF:

0.581

Gnomad AMR exome

AF:

0.295

Gnomad ASJ exome

AF:

0.298

Gnomad EAS exome

AF:

0.168

Gnomad SAS exome

AF:

0.270

Gnomad FIN exome

AF:

0.488

Gnomad NFE exome

AF:

0.411

Gnomad OTH exome

AF:

0.365

GnomAD4 exome

AF:

0.406

AC:

440908

AN:

1085050

Hom.:

63118

AF XY:

0.401

AC XY:

141946

AN XY:

354172

show subpopulations

Gnomad4 AFR exome

AF:

0.588

Gnomad4 AMR exome

AF:

0.310

Gnomad4 ASJ exome

AF:

0.300

Gnomad4 EAS exome

AF:

0.154

Gnomad4 SAS exome

AF:

0.276

Gnomad4 FIN exome

AF:

0.483

Gnomad4 NFE exome

AF:

0.421

Gnomad4 OTH exome

AF:

0.398

GnomAD4 genome

AF:

0.442

AC:

47906

AN:

108339

Hom.:

8117

Cov.:

AF XY:

0.423

AC XY:

13038

AN XY:

30815

show subpopulations

Gnomad4 AFR

AF:

0.576

Gnomad4 AMR

AF:

0.352

Gnomad4 ASJ

AF:

0.283

Gnomad4 EAS

AF:

0.176

Gnomad4 SAS

AF:

0.249

Gnomad4 FIN

AF:

0.491

Gnomad4 NFE

AF:

0.415

Gnomad4 OTH

AF:

0.408

Alfa

AF:

0.421

Hom.:

4262

Bravo

AF:

0.444

Asia WGS

AF:

0.248

AC:

628

AN:

2522

ClinVar

Significance: Benign

Submissions summary: Benign:7

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:3

Benign, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Jul 22, 2011	- -
Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Benign, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Nov 24, 2015	- -

Hypohidrotic X-linked ectodermal dysplasia

Benign:3

Benign, no assertion criteria provided	clinical testing	Natera, Inc.	Sep 16, 2020	- -
Benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Jul 30, 2021	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Mar 03, 2015

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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