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GeneBe

rs2970876

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_013261.5(PPARGC1A):c.55-2065T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.557 in 152,034 control chromosomes in the GnomAD database, including 24,820 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 0.56 ( 24820 hom., cov: 32)

Consequence

PPARGC1A
NM_013261.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.71
Variant links:
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 -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.736 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PPARGC1ANM_013261.5 linkuse as main transcriptc.55-2065T>C intron_variant ENST00000264867.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PPARGC1AENST00000264867.7 linkuse as main transcriptc.55-2065T>C intron_variant 1 NM_013261.5 P1Q9UBK2-1

Frequencies

GnomAD3 genomes
AF:
0.557
AC:
84544
AN:
151916
Hom.:
24783
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.742
Gnomad AMI
AF:
0.514
Gnomad AMR
AF:
0.529
Gnomad ASJ
AF:
0.552
Gnomad EAS
AF:
0.534
Gnomad SAS
AF:
0.482
Gnomad FIN
AF:
0.363
Gnomad MID
AF:
0.649
Gnomad NFE
AF:
0.487
Gnomad OTH
AF:
0.555
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.557
AC:
84626
AN:
152034
Hom.:
24820
Cov.:
32
AF XY:
0.549
AC XY:
40838
AN XY:
74324
show subpopulations
Gnomad4 AFR
AF:
0.743
Gnomad4 AMR
AF:
0.528
Gnomad4 ASJ
AF:
0.552
Gnomad4 EAS
AF:
0.533
Gnomad4 SAS
AF:
0.482
Gnomad4 FIN
AF:
0.363
Gnomad4 NFE
AF:
0.487
Gnomad4 OTH
AF:
0.550
Alfa
AF:
0.511
Hom.:
4252
Bravo
AF:
0.581
Asia WGS
AF:
0.508
AC:
1767
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
Cadd
Benign
7.7
Dann
Benign
0.58

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2970876; hg19: chr4-23888619; API