rs3783469
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001924.4(GADD45A):c.384+116T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.067 in 840,512 control chromosomes in the GnomAD database, including 2,067 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 0.068 ( 359 hom., cov: 34)
Exomes 𝑓: 0.067 ( 1708 hom. )
Consequence
GADD45A
NM_001924.4 intron
NM_001924.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.539
Genes affected
GADD45A (HGNC:4095): (growth arrest and DNA damage inducible alpha) This gene is a member of a group of genes whose transcript levels are increased following stressful growth arrest conditions and treatment with DNA-damaging agents. The protein encoded by this gene responds to environmental stresses by mediating activation of the p38/JNK pathway via MTK1/MEKK4 kinase. The DNA damage-induced transcription of this gene is mediated by both p53-dependent and -independent mechanisms. Alternatively spliced transcript variants encoding distinct isoforms have been found for this gene.[provided by RefSeq, Dec 2010]
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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=-0.79).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0745 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GADD45A | NM_001924.4 | c.384+116T>C | intron_variant | ENST00000370986.9 | |||
GADD45A | NM_001199741.2 | c.282+116T>C | intron_variant | ||||
GADD45A | NM_001199742.2 | c.146+577T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GADD45A | ENST00000370986.9 | c.384+116T>C | intron_variant | 1 | NM_001924.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0679 AC: 10342AN: 152202Hom.: 361 Cov.: 34
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GnomAD4 exome AF: 0.0669 AC: 46011AN: 688192Hom.: 1708 AF XY: 0.0666 AC XY: 23444AN XY: 351840
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GnomAD4 genome ? AF: 0.0679 AC: 10345AN: 152320Hom.: 359 Cov.: 34 AF XY: 0.0670 AC XY: 4994AN XY: 74488
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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
RBP_binding_hub_radar
RBP_regulation_power_radar
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