rs10517032

chr4-23966759-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001330751.2(PPARGC1A):c.70-81828G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.055 in 152,252 control chromosomes in the GnomAD database, including 297 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 0.055 (297 hom., cov: 32)
• Consequence: PPARGC1A NM_001330751.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.297

Genes affected

PPARGC1A (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.142 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PPARGC1A	NM_001330751.2	c.70-81828G>T		intron_variant
PPARGC1A	NM_001330752.2	c.19-81828G>T		intron_variant
PPARGC1A	NM_001354825.2	c.70-81828G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0550 AC: 8367 AN: 152134 Hom.: 297 Cov.: 32

Gnomad AFR AF: 0.0373

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.0412

Gnomad ASJ AF: 0.0548

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.0531

Gnomad FIN AF: 0.0369

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0628

Gnomad OTH AF: 0.0575

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

GnomAD4 genome AF: 0.0550 AC: 8372 AN: 152252 Hom.: 297 Cov.: 32 AF XY: 0.0542 AC XY: 4035 AN XY: 74438

Gnomad4 AFR AF: 0.0373

Gnomad4 AMR AF: 0.0412

Gnomad4 ASJ AF: 0.0548

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.0538

Gnomad4 FIN AF: 0.0369

Gnomad4 NFE AF: 0.0628

Gnomad4 OTH AF: 0.0569

Alfa AF: 0.0563 Hom.: 41

Bravo AF: 0.0557

Asia WGS AF: 0.0790 AC: 275 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	0.68
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10517032; hg19: chr4-23968382;