rs7680610

Positions:

• chr4-24116542-A-G
• chr4-24116542-A-T

Variant summary

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

The NM_001330751.2(PPARGC1A):​c.-99-24907T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.692 in 152,078 control chromosomes in the GnomAD database, including 36,909 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 0.69 (36909 hom., cov: 32)
• Consequence: PPARGC1A NM_001330751.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.422

Genes affected

PPARGC1A (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.801 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PPARGC1A	NM_001330751.2	c.-99-24907T>C		intron_variant
PPARGC1A	NM_001330752.2	c.18+141661T>C		intron_variant
PPARGC1A	NM_001354825.2	c.-99-24907T>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.692 AC: 105112 AN: 151960 Hom.: 36861 Cov.: 32

Gnomad AFR AF: 0.808

Gnomad AMI AF: 0.645

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.576

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.683

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.654

Gnomad OTH AF: 0.639

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

GnomAD4 genome AF: 0.692 AC: 105223 AN: 152078 Hom.: 36909 Cov.: 32 AF XY: 0.690 AC XY: 51326 AN XY: 74336

Gnomad4 AFR AF: 0.808

Gnomad4 AMR AF: 0.655

Gnomad4 ASJ AF: 0.610

Gnomad4 EAS AF: 0.575

Gnomad4 SAS AF: 0.591

Gnomad4 FIN AF: 0.683

Gnomad4 NFE AF: 0.654

Gnomad4 OTH AF: 0.639

Alfa AF: 0.649 Hom.: 57503

Bravo AF: 0.694

Asia WGS AF: 0.606 AC: 2106 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.37
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7680610; hg19: chr4-24118165;