rs60808129
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_145861.4(EDARADD):c.60G>A(p.Glu20=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0209 in 1,612,996 control chromosomes in the GnomAD database, including 2,822 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_145861.4 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EDARADD | NM_145861.4 | c.60G>A | p.Glu20= | splice_region_variant, synonymous_variant | 1/6 | ENST00000334232.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EDARADD | ENST00000334232.9 | c.60G>A | p.Glu20= | splice_region_variant, synonymous_variant | 1/6 | 1 | NM_145861.4 | ||
EDARADD | ENST00000439430.5 | c.-5-14712G>A | intron_variant | 3 | |||||
EDARADD | ENST00000637660.1 | c.-5-14712G>A | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0226 AC: 3441AN: 152152Hom.: 258 Cov.: 33
GnomAD3 exomes AF: 0.0467 AC: 11696AN: 250330Hom.: 1135 AF XY: 0.0447 AC XY: 6039AN XY: 135218
GnomAD4 exome AF: 0.0208 AC: 30339AN: 1460726Hom.: 2563 Cov.: 33 AF XY: 0.0216 AC XY: 15664AN XY: 726596
GnomAD4 genome ? AF: 0.0226 AC: 3436AN: 152270Hom.: 259 Cov.: 33 AF XY: 0.0255 AC XY: 1896AN XY: 74458
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jul 28, 2015 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 21, 2015 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Hypohidrotic Ectodermal Dysplasia, Recessive Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Ectodermal dysplasia 11B, hypohidrotic/hair/tooth type, autosomal recessive;C3541517:Ectodermal dysplasia 11A, hypohidrotic/hair/tooth type, autosomal dominant Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Hypohidrotic ectodermal dysplasia Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at