chrX-69616364-A-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The NM_001399.5(EDA):c.56A>C(p.Glu19Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000315 in 1,206,268 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 12 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. E19E) has been classified as Likely benign.
Frequency
Consequence
NM_001399.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EDA | NM_001399.5 | c.56A>C | p.Glu19Ala | missense_variant | 1/8 | ENST00000374552.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EDA | ENST00000374552.9 | c.56A>C | p.Glu19Ala | missense_variant | 1/8 | 1 | NM_001399.5 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000266 AC: 3AN: 112695Hom.: 0 Cov.: 24 AF XY: 0.0000287 AC XY: 1AN XY: 34893
GnomAD3 exomes AF: 0.0000291 AC: 5AN: 171825Hom.: 0 AF XY: 0.0000488 AC XY: 3AN XY: 61511
GnomAD4 exome AF: 0.0000320 AC: 35AN: 1093573Hom.: 0 Cov.: 31 AF XY: 0.0000305 AC XY: 11AN XY: 360855
GnomAD4 genome ? AF: 0.0000266 AC: 3AN: 112695Hom.: 0 Cov.: 24 AF XY: 0.0000287 AC XY: 1AN XY: 34893
ClinVar
Submissions by phenotype
Hypohidrotic X-linked ectodermal dysplasia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 11, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at