rs4407488

Variant names:

• chr4-24434844-T-A
• rs4407488
• NM_001330751.2:c.-165+37531A>T

Variant summary

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

The NM_001330751.2(PPARGC1A):​c.-165+37531A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.464 in 152,030 control chromosomes in the GnomAD database, including 17,007 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 0.46 (17007 hom., cov: 32)
• Consequence: PPARGC1A NM_001330751.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.559
• Publications: 0 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.572 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PPARGC1A	NM_001330751.2	c.-165+37531A>T		intron_variant	Intron 1 of 14		NP_001317680.1
PPARGC1A	NM_001354825.2	c.-100+37531A>T		intron_variant	Intron 1 of 13		NP_001341754.1
PPARGC1A	NM_001354827.2	c.-100+37531A>T		intron_variant	Intron 1 of 13		NP_001341756.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.464 AC: 70522 AN: 151912 Hom.: 16981 Cov.: 32

Gnomad AFR AF: 0.578

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.464 AC: 70597 AN: 152030 Hom.: 17007 Cov.: 32 AF XY: 0.466 AC XY: 34588 AN XY: 74288

African (AFR) AF: 0.579 AC: 23987 AN: 41456

American (AMR) AF: 0.383 AC: 5850 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.356 AC: 1237 AN: 3470

East Asian (EAS) AF: 0.415 AC: 2136 AN: 5150

South Asian (SAS) AF: 0.356 AC: 1718 AN: 4820

European-Finnish (FIN) AF: 0.537 AC: 5667 AN: 10556

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.422 AC: 28675 AN: 67976

Other (OTH) AF: 0.443 AC: 935 AN: 2110

Alfa AF: 0.456 Hom.: 1991

Bravo AF: 0.460

Asia WGS AF: 0.407 AC: 1416 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.28
DANN	Benign	0.72
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs4407488; hg19: chr4-24436467;