rs7672552

chr4-24009985-C-T

Variant summary

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

The NM_001330751.2(PPARGC1A):c.69+81483G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.574 in 151,962 control chromosomes in the GnomAD database, including 25,703 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 0.57 (25703 hom., cov: 32)
• Consequence: PPARGC1A NM_001330751.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0330

Genes affected

PPARGC1A (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.662 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PPARGC1A	NM_001330751.2	c.69+81483G>A		intron_variant
PPARGC1A	NM_001330752.2	c.19-125054G>A		intron_variant
PPARGC1A	NM_001354825.2	c.69+81483G>A		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.574 AC: 87228 AN: 151844 Hom.: 25697 Cov.: 32

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.342

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.580

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.579

Gnomad OTH AF: 0.540

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

GnomAD4 genome AF: 0.574 AC: 87265 AN: 151962 Hom.: 25703 Cov.: 32 AF XY: 0.567 AC XY: 42127 AN XY: 74264

Gnomad4 AFR AF: 0.669

Gnomad4 AMR AF: 0.440

Gnomad4 ASJ AF: 0.529

Gnomad4 EAS AF: 0.342

Gnomad4 SAS AF: 0.415

Gnomad4 FIN AF: 0.580

Gnomad4 NFE AF: 0.579

Gnomad4 OTH AF: 0.535

Alfa AF: 0.563 Hom.: 50245

Bravo AF: 0.567

Asia WGS AF: 0.368 AC: 1283 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	2.0
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7672552; hg19: chr4-24011608;