rs4253772
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_005036.6(PPARA):c.712-86C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0961 in 1,377,132 control chromosomes in the GnomAD database, including 7,188 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 0.077 ( 590 hom., cov: 32)
Exomes 𝑓: 0.098 ( 6598 hom. )
Consequence
PPARA
NM_005036.6 intron
NM_005036.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -3.33
Genes affected
PPARA (HGNC:9232): (peroxisome proliferator activated receptor alpha) Peroxisome proliferators include hypolipidemic drugs, herbicides, leukotriene antagonists, and plasticizers; this term arises because they induce an increase in the size and number of peroxisomes. Peroxisomes are subcellular organelles found in plants and animals that contain enzymes for respiration and for cholesterol and lipid metabolism. The action of peroxisome proliferators is thought to be mediated via specific receptors, called PPARs, which belong to the steroid hormone receptor superfamily. PPARs affect the expression of target genes involved in cell proliferation, cell differentiation and in immune and inflammation responses. Three closely related subtypes (alpha, beta/delta, and gamma) have been identified. This gene encodes the subtype PPAR-alpha, which is a nuclear transcription factor. Multiple alternatively spliced transcript variants have been described for this gene, although the full-length nature of only two has been determined. [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=-0.92).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PPARA | NM_005036.6 | c.712-86C>T | intron_variant | ENST00000407236.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPARA | ENST00000407236.6 | c.712-86C>T | intron_variant | 1 | NM_005036.6 | P1 | |||
PPARA | ENST00000402126.1 | c.712-86C>T | intron_variant | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0772 AC: 11752AN: 152130Hom.: 590 Cov.: 32
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GnomAD4 exome AF: 0.0984 AC: 120547AN: 1224882Hom.: 6598 AF XY: 0.0978 AC XY: 60046AN XY: 613822
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GnomAD4 genome ? AF: 0.0772 AC: 11749AN: 152250Hom.: 590 Cov.: 32 AF XY: 0.0748 AC XY: 5570AN XY: 74432
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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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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at