rs751704449
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 4P and 2B. PM1PM2BP4_Moderate
The NM_145861.4(EDARADD):c.199A>T(p.Asn67Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000658 in 152,062 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_145861.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EDARADD | NM_145861.4 | c.199A>T | p.Asn67Tyr | missense_variant | 4/6 | ENST00000334232.9 | NP_665860.2 | |
EDARADD | NM_080738.4 | c.169A>T | p.Asn57Tyr | missense_variant | 4/6 | NP_542776.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EDARADD | ENST00000334232.9 | c.199A>T | p.Asn67Tyr | missense_variant | 4/6 | 1 | NM_145861.4 | ENSP00000335076 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152062Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000400 AC: 1AN: 249694Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135020
GnomAD4 exome Cov.: 33
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152062Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74272
ClinVar
Submissions by phenotype
Ectodermal dysplasia 11B, hypohidrotic/hair/tooth type, autosomal recessive;C3541517:Ectodermal dysplasia 11A, hypohidrotic/hair/tooth type, autosomal dominant Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Aug 14, 2020 | Algorithms developed to predict the effect of missense changes on protein structure and function do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). This sequence change replaces asparagine with tyrosine at codon 67 of the EDARADD protein (p.Asn67Tyr). The asparagine residue is moderately conserved and there is a large physicochemical difference between asparagine and tyrosine. This variant is present in population databases (rs751704449, ExAC 0.002%). This variant has not been reported in the literature in individuals with EDARADD-related disease. 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