NM_145861.4:c.62-131_62-129delAAA
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BS1
The NM_145861.4(EDARADD):c.62-131_62-129delAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00612 in 202,222 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0 ( 0 hom., cov: 28)
Exomes 𝑓: 0.0061 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
EDARADD
NM_145861.4 intron
NM_145861.4 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.336
Genes affected
EDARADD (HGNC:14341): (EDAR associated via death domain) This gene was identified by its association with ectodermal dysplasia, a genetic disorder characterized by defective development of hair, teeth, and eccrine sweat glands. The protein encoded by this gene is a death domain-containing protein, and is found to interact with EDAR, a death domain receptor known to be required for the development of hair, teeth and other ectodermal derivatives. This protein and EDAR are coexpressed in epithelial cells during the formation of hair follicles and teeth. Through its interaction with EDAR, this protein acts as an adaptor, and links the receptor to downstream signaling pathways. Two alternatively spliced transcript variants of this gene encoding distinct isoforms have been reported. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BS1
Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.00612 (1238/202222) while in subpopulation MID AF= 0.0093 (8/860). AF 95% confidence interval is 0.00728. There are 0 homozygotes in gnomad4_exome. There are 645 alleles in male gnomad4_exome subpopulation. This position pass quality control queck.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| EDARADD | NM_145861.4 | c.62-131_62-129delAAA | intron_variant | Intron 1 of 5 | ENST00000334232.9 | NP_665860.2 | ||
| EDARADD | NM_080738.5 | c.32-131_32-129delAAA | intron_variant | Intron 1 of 5 | NP_542776.1 | |||
| EDARADD | NM_001422628.1 | c.-5-131_-5-129delAAA | intron_variant | Intron 3 of 7 | NP_001409557.1 |
Ensembl
Frequencies
GnomAD3 genomes 0.00 AC: 0AN: 129100Hom.: 0 Cov.: 28 FAILED QC
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GnomAD4 exome AF: 0.00612 AC: 1238AN: 202222Hom.: 0 AF XY: 0.00607 AC XY: 645AN XY: 106194
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GnomAD4 genome 0.00 AC: 0AN: 129100Hom.: 0 Cov.: 28 AF XY: 0.00 AC XY: 0AN XY: 61768
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ClinVar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at