rs1054564
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004864.4(GDF15):c.*70G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 1,072,570 control chromosomes in the GnomAD database, including 10,156 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 ( 1111 hom., cov: 32)
Exomes 𝑓: 0.13 ( 9045 hom. )
Consequence
GDF15
NM_004864.4 3_prime_UTR
NM_004864.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.849
Genes affected
GDF15 (HGNC:30142): (growth differentiation factor 15) This gene encodes a secreted ligand of the TGF-beta (transforming growth factor-beta) superfamily of proteins. Ligands of this family bind various TGF-beta receptors leading to recruitment and activation of SMAD family transcription factors that regulate gene expression. The encoded preproprotein is proteolytically processed to generate each subunit of the disulfide-linked homodimer. The protein is expressed in a broad range of cell types, acts as a pleiotropic cytokine and is involved in the stress response program of cells after cellular injury. Increased protein levels are associated with disease states such as tissue hypoxia, inflammation, acute injury and oxidative stress. [provided by RefSeq, Aug 2016]
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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 (EAS) allele frequency at 95% confidence interval = 0.161 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GDF15 | NM_004864.4 | c.*70G>C | 3_prime_UTR_variant | 2/2 | ENST00000252809.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GDF15 | ENST00000252809.3 | c.*70G>C | 3_prime_UTR_variant | 2/2 | 1 | NM_004864.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.110 AC: 16702AN: 152148Hom.: 1112 Cov.: 32
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GnomAD4 exome AF: 0.135 AC: 124035AN: 920304Hom.: 9045 Cov.: 12 AF XY: 0.135 AC XY: 62680AN XY: 464434
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GnomAD4 genome ? AF: 0.110 AC: 16700AN: 152266Hom.: 1111 Cov.: 32 AF XY: 0.108 AC XY: 8069AN XY: 74452
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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