X-69616336-G-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_001399.5(EDA):c.28G>C(p.Glu10Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000666 in 1,201,514 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E10K) has been classified as Uncertain significance.
Frequency
Consequence
NM_001399.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EDA | NM_001399.5 | c.28G>C | p.Glu10Gln | missense_variant | 1/8 | ENST00000374552.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EDA | ENST00000374552.9 | c.28G>C | p.Glu10Gln | missense_variant | 1/8 | 1 | NM_001399.5 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000177 AC: 2AN: 112958Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0AN XY: 35098
GnomAD3 exomes AF: 0.0000124 AC: 2AN: 160951Hom.: 0 AF XY: 0.0000363 AC XY: 2AN XY: 55115
GnomAD4 exome AF: 0.00000551 AC: 6AN: 1088556Hom.: 0 Cov.: 31 AF XY: 0.00000558 AC XY: 2AN XY: 358600
GnomAD4 genome ? AF: 0.0000177 AC: 2AN: 112958Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0AN XY: 35098
ClinVar
Submissions by phenotype
Hypohidrotic X-linked ectodermal dysplasia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 08, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at