chrX-70028046-CCT-C
Variant summary
Our verdict is Benign. The variant received -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_001399.5(EDA):c.706+11_706+12delCT 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
NM_001399.5 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.988
Publications
2 publications found
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 Gene-Disease associations (from GenCC):
- tooth agenesis, selective, X-linked, 1Inheritance: XL Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P
- X-linked hypohidrotic ectodermal dysplasiaInheritance: XL Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: G2P, Orphanet, Labcorp Genetics (formerly Invitae)
- tooth agenesisInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -16 ACMG points.
BP6
Variant X-70028046-CCT-C is Benign according to our data. Variant chrX-70028046-CCT-C is described in CliVar as Benign. Clinvar id is 44204.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-70028046-CCT-C is described in CliVar as Benign. Clinvar id is 44204.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-70028046-CCT-C is described in CliVar as Benign. Clinvar id is 44204.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-70028046-CCT-C is described in CliVar as Benign. Clinvar id is 44204.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-70028046-CCT-C is described in CliVar as Benign. Clinvar id is 44204.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-70028046-CCT-C is described in CliVar as Benign. Clinvar id is 44204.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-70028046-CCT-C is described in CliVar as Benign. Clinvar id is 44204.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-70028046-CCT-C is described in CliVar as Benign. Clinvar id is 44204.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-70028046-CCT-C is described in CliVar as Benign. Clinvar id is 44204.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-70028046-CCT-C is described in CliVar 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
Ensembl
Frequencies
GnomAD3 genomes AF: 0.442 AC: 47876AN: 108293Hom.: 8118 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
47876
AN:
108293
Hom.:
Cov.:
0
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD2 exomes AF: 0.371 AC: 57799AN: 155702 AF XY: 0.356 show subpopulations
GnomAD2 exomes
AF:
AC:
57799
AN:
155702
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.406 AC: 440908AN: 1085050Hom.: 63118 AF XY: 0.401 AC XY: 141946AN XY: 354172 show subpopulations
GnomAD4 exome
AF:
AC:
440908
AN:
1085050
Hom.:
AF XY:
AC XY:
141946
AN XY:
354172
show subpopulations
African (AFR)
AF:
AC:
15244
AN:
25928
American (AMR)
AF:
AC:
10558
AN:
34104
Ashkenazi Jewish (ASJ)
AF:
AC:
5736
AN:
19115
East Asian (EAS)
AF:
AC:
4537
AN:
29488
South Asian (SAS)
AF:
AC:
14431
AN:
52202
European-Finnish (FIN)
AF:
AC:
19171
AN:
39727
Middle Eastern (MID)
AF:
AC:
1247
AN:
3162
European-Non Finnish (NFE)
AF:
AC:
351872
AN:
835856
Other (OTH)
AF:
AC:
18112
AN:
45468
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.472
Heterozygous variant carriers
0
8676
17351
26027
34702
43378
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
11694
23388
35082
46776
58470
<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 AF: 0.442 AC: 47906AN: 108339Hom.: 8117 Cov.: 0 AF XY: 0.423 AC XY: 13038AN XY: 30815 show subpopulations
GnomAD4 genome
AF:
AC:
47906
AN:
108339
Hom.:
Cov.:
0
AF XY:
AC XY:
13038
AN XY:
30815
show subpopulations
African (AFR)
AF:
AC:
17027
AN:
29568
American (AMR)
AF:
AC:
3620
AN:
10270
Ashkenazi Jewish (ASJ)
AF:
AC:
740
AN:
2613
East Asian (EAS)
AF:
AC:
602
AN:
3420
South Asian (SAS)
AF:
AC:
612
AN:
2455
European-Finnish (FIN)
AF:
AC:
2709
AN:
5514
Middle Eastern (MID)
AF:
AC:
78
AN:
210
European-Non Finnish (NFE)
AF:
AC:
21652
AN:
52139
Other (OTH)
AF:
AC:
608
AN:
1489
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.495
Heterozygous variant carriers
0
920
1840
2761
3681
4601
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
444
888
1332
1776
2220
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
628
AN:
2522
ClinVar
Significance: Benign
Submissions summary: Benign:7
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Hypohidrotic X-linked ectodermal dysplasia Benign:3
Jul 30, 2021
Genome-Nilou Lab
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Sep 16, 2020
Natera, Inc.
Significance:Benign
Review Status:no assertion criteria provided
Collection Method:clinical testing
- -
Feb 03, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
not specified Benign:3
Nov 24, 2015
Eurofins Ntd Llc (ga)
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Jul 22, 2011
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
-
PreventionGenetics, part of Exact Sciences
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
not provided Benign:1
Mar 03, 2015
GeneDx
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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