4-23815786-G-A

Variant names:

• chr4-23815786-G-A
• rs2932968
• NM_013261.5:c.878-1181C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_013261.5(PPARGC1A):​c.878-1181C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.839 in 152,124 control chromosomes in the GnomAD database, including 53,969 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 0.84 (53969 hom., cov: 31)
• Consequence: PPARGC1A NM_013261.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0580
• Publications: 4 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.94 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_013261.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPARGC1A	NM_013261.5	MANE Select	c.878-1181C>T		intron	N/A	NP_037393.1
	PPARGC1A	NM_001330751.2		c.893-1181C>T		intron	N/A	NP_001317680.1
	PPARGC1A	NM_001354825.2		c.893-1181C>T		intron	N/A	NP_001341754.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPARGC1A	ENST00000264867.7	TSL:1 MANE Select	c.878-1181C>T		intron	N/A	ENSP00000264867.2
	PPARGC1A	ENST00000613098.4	TSL:1	c.497-1181C>T		intron	N/A	ENSP00000481498.1
	PPARGC1A	ENST00000506055.5	TSL:1	n.*93-1181C>T		intron	N/A	ENSP00000423075.1

Frequencies

GnomAD3 genomes AF: 0.839 AC: 127469 AN: 152006 Hom.: 53907 Cov.: 31

Gnomad AFR AF: 0.948

Gnomad AMI AF: 0.746

Gnomad AMR AF: 0.866

Gnomad ASJ AF: 0.849

Gnomad EAS AF: 0.770

Gnomad SAS AF: 0.825

Gnomad FIN AF: 0.814

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.776

Gnomad OTH AF: 0.849

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.839 AC: 127591 AN: 152124 Hom.: 53969 Cov.: 31 AF XY: 0.841 AC XY: 62537 AN XY: 74344

African (AFR) AF: 0.948 AC: 39370 AN: 41540

American (AMR) AF: 0.866 AC: 13239 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.849 AC: 2946 AN: 3470

East Asian (EAS) AF: 0.770 AC: 3952 AN: 5134

South Asian (SAS) AF: 0.824 AC: 3975 AN: 4822

European-Finnish (FIN) AF: 0.814 AC: 8607 AN: 10568

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.776 AC: 52781 AN: 67996

Other (OTH) AF: 0.851 AC: 1795 AN: 2110

Alfa AF: 0.828 Hom.: 8252

Bravo AF: 0.847

Asia WGS AF: 0.848 AC: 2949 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.2
DANN	Benign	0.63
PhyloP100		0.058
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2932968; hg19: chr4-23817409;