4-23822643-A-T

Variant names:

• chr4-23822643-A-T
• rs2932977
• NM_013261.5:c.877+1637T>A

Variant summary

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

The NM_013261.5(PPARGC1A):​c.877+1637T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.831 in 152,046 control chromosomes in the GnomAD database, including 52,646 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 0.83 (52646 hom., cov: 32)
• Consequence: PPARGC1A NM_013261.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.299
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.873 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PPARGC1A	NM_013261.5	c.877+1637T>A		intron_variant	Intron 7 of 12	ENST00000264867.7	NP_037393.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPARGC1A	ENST00000264867.7	c.877+1637T>A		intron_variant	Intron 7 of 12	1	NM_013261.5	ENSP00000264867.2

Frequencies

GnomAD3 genomes AF: 0.831 AC: 126221 AN: 151928 Hom.: 52590 Cov.: 32

Gnomad AFR AF: 0.880

Gnomad AMI AF: 0.746

Gnomad AMR AF: 0.871

Gnomad ASJ AF: 0.859

Gnomad EAS AF: 0.776

Gnomad SAS AF: 0.841

Gnomad FIN AF: 0.841

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.793

Gnomad OTH AF: 0.846

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

GnomAD4 genome AF: 0.831 AC: 126336 AN: 152046 Hom.: 52646 Cov.: 32 AF XY: 0.834 AC XY: 61994 AN XY: 74324

African (AFR) AF: 0.880 AC: 36524 AN: 41498

American (AMR) AF: 0.872 AC: 13287 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.859 AC: 2979 AN: 3468

East Asian (EAS) AF: 0.775 AC: 3992 AN: 5148

South Asian (SAS) AF: 0.840 AC: 4049 AN: 4820

European-Finnish (FIN) AF: 0.841 AC: 8903 AN: 10588

Middle Eastern (MID) AF: 0.867 AC: 255 AN: 294

European-Non Finnish (NFE) AF: 0.793 AC: 53882 AN: 67970

Other (OTH) AF: 0.847 AC: 1786 AN: 2108

Alfa AF: 0.821 Hom.: 6369

Bravo AF: 0.834

Asia WGS AF: 0.850 AC: 2952 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.93
DANN	Benign	0.61
PhyloP100		-0.30
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: rs2932977; hg19: chr4-23824266;