rs3046000
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
The NM_001924.4(GADD45A):c.385-73_385-65del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00646 in 916,474 control chromosomes in the GnomAD database, including 231 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.024 ( 163 hom., cov: 33)
Exomes 𝑓: 0.0030 ( 68 hom. )
Consequence
GADD45A
NM_001924.4 intron
NM_001924.4 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.28
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 -8 ACMG points.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0809 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GADD45A | NM_001924.4 | c.385-73_385-65del | intron_variant | ENST00000370986.9 | |||
GADD45A | NM_001199741.2 | c.283-73_283-65del | intron_variant | ||||
GADD45A | NM_001199742.2 | c.147-73_147-65del | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GADD45A | ENST00000370986.9 | c.385-73_385-65del | intron_variant | 1 | NM_001924.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0239 AC: 3634AN: 152164Hom.: 162 Cov.: 33
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GnomAD4 exome AF: 0.00299 AC: 2285AN: 764194Hom.: 68 AF XY: 0.00252 AC XY: 1010AN XY: 401442
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GnomAD4 genome ? AF: 0.0239 AC: 3636AN: 152280Hom.: 163 Cov.: 33 AF XY: 0.0229 AC XY: 1705AN XY: 74476
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ClinVar
Not reported inComputational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at