chrX-70035434-G-A

Position:

chrX-70035434-G-A

Variant summary

Our verdict is Benign. Variant got -18 ACMG points: 2P and 20B. PM1BP4_StrongBP6_Very_StrongBS1BS2

The ENST00000374552.9(EDA):c.1001G>A(p.Arg334His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000382 in 1,207,703 control chromosomes in the GnomAD database, including 4 homozygotes. There are 137 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R334C) has been classified as Benign.

Frequency

Genomes: 𝑓 0.00065 ( 1 hom., 22 hem., cov: 21)

Exomes 𝑓: 0.00035 ( 3 hom. 115 hem. )

Consequence

EDA
ENST00000374552.9 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts P:1B:8

Conservation

PhyloP100: 9.25

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -18 ACMG points.

PM1

In a hotspot region, there are 4 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 1 benign, 2 uncertain in ENST00000374552.9

BP4

Computational evidence support a benign effect (MetaRNN=0.010842383).

BP6

Variant X-70035434-G-A is Benign according to our data. Variant chrX-70035434-G-A is described in ClinVar as [Benign]. Clinvar id is 253055.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-70035434-G-A is described in Lovd as [Likely_benign].

BS1

Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.000654 (72/110131) while in subpopulation EAS AF= 0.0146 (51/3501). AF 95% confidence interval is 0.0114. There are 1 homozygotes in gnomad4. There are 22 alleles in male gnomad4 subpopulation. Median coverage is 21. This position pass quality control queck.

BS2

High Hemizygotes in GnomAd4 at 22 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EDA	NM_001399.5 linkuse as main transcript	c.1001G>A	p.Arg334His	missense_variant	8/8	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.1001G>A	p.Arg334His	missense_variant	8/8	1	NM_001399.5	ENSP00000363680	P4	Q92838-1
EDA	ENST00000374553.6 linkuse as main transcript	c.995G>A	p.Arg332His	missense_variant	8/8	1		ENSP00000363681	A1	Q92838-3
EDA	ENST00000524573.5 linkuse as main transcript	c.986G>A	p.Arg329His	missense_variant	8/8	1		ENSP00000432585	A1	Q92838-9
EDA	ENST00000616899.1 linkuse as main transcript	c.605G>A	p.Arg202His	missense_variant	7/7	5		ENSP00000481963

Frequencies

GnomAD3 genomes

AF:

0.000663

AC:

AN:

110077

Hom.:

Cov.:

AF XY:

0.000711

AC XY:

AN XY:

32331

show subpopulations

Gnomad AFR

AF:

0.000265

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000970

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.0148

Gnomad SAS

AF:

0.000396

Gnomad FIN

AF:

0.000345

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000152

Gnomad OTH

AF:

0.000678

GnomAD3 exomes

AF:

0.000920

AC:

166

AN:

180407

Hom.:

AF XY:

0.000705

AC XY:

AN XY:

65265

show subpopulations

Gnomad AFR exome

AF:

0.000539

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00999

Gnomad SAS exome

AF:

0.000373

Gnomad FIN exome

AF:

0.000253

Gnomad NFE exome

AF:

0.0000500

Gnomad OTH exome

AF:

0.00157

GnomAD4 exome

AF:

0.000354

AC:

389

AN:

1097572

Hom.:

Cov.:

AF XY:

0.000317

AC XY:

115

AN XY:

362942

show subpopulations

Gnomad4 AFR exome

AF:

0.000152

Gnomad4 AMR exome

AF:

0.0000284

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00504

Gnomad4 SAS exome

AF:

0.000444

Gnomad4 FIN exome

AF:

0.000247

Gnomad4 NFE exome

AF:

0.000170

Gnomad4 OTH exome

AF:

0.00119

GnomAD4 genome

AF:

0.000654

AC:

AN:

110131

Hom.:

Cov.:

AF XY:

0.000679

AC XY:

AN XY:

32395

show subpopulations

Gnomad4 AFR

AF:

0.000265

Gnomad4 AMR

AF:

0.0000969

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.0146

Gnomad4 SAS

AF:

0.000397

Gnomad4 FIN

AF:

0.000345

Gnomad4 NFE

AF:

0.000152

Gnomad4 OTH

AF:

0.000669

Alfa

AF:

0.000294

Hom.:

Bravo

AF:

0.000491

TwinsUK

AF:

0.000270

AC:

ALSPAC

AF:

0.00

AC:

ESP6500AA

AF:

0.000522

AC:

ESP6500EA

AF:

0.000149

AC:

ExAC

AF:

0.000692

AC:

ClinVar

Significance: Benign

Submissions summary: Pathogenic:1Benign:8

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Likely benign, no assertion criteria provided	clinical testing	Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)	-	- -
Likely benign, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Dec 01, 2023	EDA: BS1, BS2 -

Tooth agenesis, selective, X-linked, 1

Pathogenic:1Benign:1

Pathogenic, no assertion criteria provided	literature only	OMIM	Aug 17, 2016	- -
Benign, no assertion criteria provided	curation	Reproductive Health Research and Development, BGI Genomics	Jan 06, 2020	NM_001399.4:c.1001G>A in EDA gene has an allele frequency of 0.011 in East Asian subpopulation in the gnomAD database, including 2 homozygous occurrences, and 54 hemizygotes. This variant was reported in a male patient with Non-syndromic Oligodontia, inherited from his mother, which indicated a X-linked recessive inheritance (PMID: 19278982). Taken together, we interprete this variant as Benign/Likely benign variant. ACMG/AMP criteria applied: BS1, BS2. -

Hypohidrotic X-linked ectodermal dysplasia

Benign:2

Benign, no assertion criteria provided	clinical testing	Natera, Inc.	Jul 23, 2020	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 27, 2024	- -

Hypohidrotic X-linked ectodermal dysplasia;C1970757:Tooth agenesis, selective, X-linked, 1

Benign:1

Benign, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Nov 05, 2021

- -

See cases

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein

Feb 17, 2020

ACMG classification criteria: BS1, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.87

BayesDel_addAF

Uncertain

0.074

BayesDel_noAF

Pathogenic

0.34

CADD

Pathogenic

DANN

Uncertain

1.0

DEOGEN2

Uncertain

0.76

.;D;.;.

FATHMM_MKL

Pathogenic

0.99

LIST_S2

Pathogenic

0.99

D;D;D;D

MetaRNN

Benign

0.011

T;T;T;T

MetaSVM

Uncertain

0.74

MutationAssessor

Benign

1.2

.;L;.;.

MutationTaster

Benign

1.0

D;D;D

PrimateAI

Uncertain

0.69

PROVEAN

Benign

-1.3

N;N;N;.

REVEL

Pathogenic

0.77

Sift

Uncertain

0.025

D;.;.;.

Sift4G

Uncertain

0.044

D;T;D;T

Polyphen

1.0

D;D;D;.

Vest4

0.26

MVP

1.0

MPC

1.5

ClinPred

0.058

GERP RS

5.5

Varity_R

0.89

gMVP

0.86

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