rs2946385
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_013261.5(PPARGC1A):c.234+52C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000236 in 1,523,946 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.00014 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000011 ( 0 hom. )
Consequence
PPARGC1A
NM_013261.5 intron
NM_013261.5 intron
Scores
7
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.85
Genes affected
PPARGC1A (HGNC:9237): (PPARG coactivator 1 alpha) The protein encoded by this gene is a transcriptional coactivator that regulates the genes involved in energy metabolism. This protein interacts with PPARgamma, which permits the interaction of this protein with multiple transcription factors. This protein can interact with, and regulate the activities of, cAMP response element binding protein (CREB) and nuclear respiratory factors (NRFs). It provides a direct link between external physiological stimuli and the regulation of mitochondrial biogenesis, and is a major factor that regulates muscle fiber type determination. This protein may be also involved in controlling blood pressure, regulating cellular cholesterol homoeostasis, and the development of obesity. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_addAF=-0.697914).
BS2
?
High AC in GnomAd4 at 21 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PPARGC1A | NM_013261.5 | c.234+52C>T | intron_variant | ENST00000264867.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPARGC1A | ENST00000264867.7 | c.234+52C>T | intron_variant | 1 | NM_013261.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000138 AC: 21AN: 151966Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000548 AC: 12AN: 219080Hom.: 0 AF XY: 0.0000339 AC XY: 4AN XY: 118046
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GnomAD4 exome AF: 0.0000109 AC: 15AN: 1371862Hom.: 0 Cov.: 24 AF XY: 0.0000118 AC XY: 8AN XY: 679368
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GnomAD4 genome ? AF: 0.000138 AC: 21AN: 152084Hom.: 0 Cov.: 33 AF XY: 0.0000807 AC XY: 6AN XY: 74332
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
MutationTaster
Benign
P;P
Vest4
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RBP_binding_hub_radar
RBP_regulation_power_radar
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