chrX-70035434-G-A
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 2P and 20B. PM1BP4_StrongBP6_Very_StrongBS1BS2
The NM_001399.5(EDA):c.1001G>A(p.Arg334His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000382 in 1,207,703 control chromosomes in the GnomAD database, including 4 homozygotes. There are 137 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001399.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EDA | ENST00000374552.9 | c.1001G>A | p.Arg334His | missense_variant | Exon 8 of 8 | 1 | NM_001399.5 | ENSP00000363680.4 | ||
EDA | ENST00000374553.6 | c.995G>A | p.Arg332His | missense_variant | Exon 8 of 8 | 1 | ENSP00000363681.2 | |||
EDA | ENST00000524573.5 | c.986G>A | p.Arg329His | missense_variant | Exon 8 of 8 | 1 | ENSP00000432585.1 | |||
EDA | ENST00000616899.1 | c.605G>A | p.Arg202His | missense_variant | Exon 7 of 7 | 5 | ENSP00000481963.1 |
Frequencies
GnomAD3 genomes AF: 0.000663 AC: 73AN: 110077Hom.: 1 Cov.: 21 AF XY: 0.000711 AC XY: 23AN XY: 32331
GnomAD3 exomes AF: 0.000920 AC: 166AN: 180407Hom.: 2 AF XY: 0.000705 AC XY: 46AN XY: 65265
GnomAD4 exome AF: 0.000354 AC: 389AN: 1097572Hom.: 3 Cov.: 31 AF XY: 0.000317 AC XY: 115AN XY: 362942
GnomAD4 genome AF: 0.000654 AC: 72AN: 110131Hom.: 1 Cov.: 21 AF XY: 0.000679 AC XY: 22AN XY: 32395
ClinVar
Submissions by phenotype
not provided Benign:3
- -
EDA: BS1, BS2 -
- -
Tooth agenesis, selective, X-linked, 1 Pathogenic:1Benign:1
- -
NM_001399.4:c.1001G>A in EDA gene has an allele frequency of 0.011 in East Asian subpopulation in the gnomAD database, including 2 homozygous occurrences, and 54 hemizygotes. This variant was reported in a male patient with Non-syndromic Oligodontia, inherited from his mother, which indicated a X-linked recessive inheritance (PMID: 19278982). Taken together, we interprete this variant as Benign/Likely benign variant. ACMG/AMP criteria applied: BS1, BS2. -
Hypohidrotic X-linked ectodermal dysplasia Benign:2
- -
- -
Hypohidrotic X-linked ectodermal dysplasia;C1970757:Tooth agenesis, selective, X-linked, 1 Benign:1
- -
See cases Benign:1
ACMG classification criteria: BS1, BS2 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at