chr1-236409089-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_145861.4(EDARADD):c.62-127G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.664 in 437,550 control chromosomes in the GnomAD database, including 100,309 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.68 ( 34701 hom., cov: 27)
Exomes 𝑓: 0.66 ( 65608 hom. )
Consequence
EDARADD
NM_145861.4 intron
NM_145861.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.990
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 Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BP6
?
Variant 1-236409089-G-A is Benign according to our data. Variant chr1-236409089-G-A is described in ClinVar as [Benign]. Clinvar id is 1295882.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EDARADD | NM_145861.4 | c.62-127G>A | intron_variant | ENST00000334232.9 | |||
EDARADD | NM_080738.4 | c.32-127G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EDARADD | ENST00000334232.9 | c.62-127G>A | intron_variant | 1 | NM_145861.4 |
Frequencies
GnomAD3 genomes ? AF: 0.677 AC: 101367AN: 149752Hom.: 34655 Cov.: 27
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GnomAD4 exome AF: 0.657 AC: 188946AN: 287718Hom.: 65608 AF XY: 0.657 AC XY: 98907AN XY: 150496
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GnomAD4 genome ? AF: 0.677 AC: 101463AN: 149832Hom.: 34701 Cov.: 27 AF XY: 0.679 AC XY: 49648AN XY: 73164
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 11, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at