X-69616319-C-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_001399.5(EDA):āc.11C>Gā(p.Pro4Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000259 in 1,195,048 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 14 hemizygotes in GnomAD. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001399.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000887 AC: 1AN: 112785Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0AN XY: 34937
GnomAD4 exome AF: 0.0000277 AC: 30AN: 1082263Hom.: 0 Cov.: 31 AF XY: 0.0000394 AC XY: 14AN XY: 355225
GnomAD4 genome AF: 0.00000887 AC: 1AN: 112785Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0AN XY: 34937
ClinVar
Submissions by phenotype
Hypohidrotic X-linked ectodermal dysplasia Uncertain:1
This sequence change replaces proline, which is neutral and non-polar, with arginine, which is basic and polar, at codon 4 of the EDA protein (p.Pro4Arg). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with EDA-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Not Available"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at