rs2290149
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000706887.1(MADD):c.4615+28T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 1,612,614 control chromosomes in the GnomAD database, including 16,335 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.11 ( 1004 hom., cov: 32)
Exomes 𝑓: 0.14 ( 15331 hom. )
Consequence
MADD
ENST00000706887.1 intron
ENST00000706887.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.04
Genes affected
MADD (HGNC:6766): (MAP kinase activating death domain) Tumor necrosis factor alpha (TNF-alpha) is a signaling molecule that interacts with one of two receptors on cells targeted for apoptosis. The apoptotic signal is transduced inside these cells by cytoplasmic adaptor proteins. The protein encoded by this gene is a death domain-containing adaptor protein that interacts with the death domain of TNF-alpha receptor 1 to activate mitogen-activated protein kinase (MAPK) and propagate the apoptotic signal. It is membrane-bound and expressed at a higher level in neoplastic cells than in normal cells. Several transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MADD | NM_001376571.1 | c.4615+28T>C | intron_variant | ENST00000706887.1 | |||
MADD | NR_164835.1 | n.4805+28T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MADD | ENST00000706887.1 | c.4615+28T>C | intron_variant | NM_001376571.1 |
Frequencies
GnomAD3 genomes ? AF: 0.107 AC: 16282AN: 152102Hom.: 1008 Cov.: 32
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GnomAD3 exomes AF: 0.126 AC: 31624AN: 250522Hom.: 2405 AF XY: 0.133 AC XY: 18066AN XY: 135396
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GnomAD4 exome AF: 0.140 AC: 204030AN: 1460394Hom.: 15331 Cov.: 31 AF XY: 0.142 AC XY: 103368AN XY: 726520
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GnomAD4 genome ? AF: 0.107 AC: 16275AN: 152220Hom.: 1004 Cov.: 32 AF XY: 0.107 AC XY: 7956AN XY: 74440
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at