rs6832344

chr4-24055913-A-G

Variant summary

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

The NM_001330751.2(PPARGC1A):c.69+35555T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 152,176 control chromosomes in the GnomAD database, including 10,299 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 0.36 (10299 hom., cov: 33)
• Consequence: PPARGC1A NM_001330751.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

Genes affected

PPARGC1A (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PPARGC1A	NM_001330751.2	c.69+35555T>C		intron_variant
PPARGC1A	NM_001330752.2	c.19-170982T>C		intron_variant
PPARGC1A	NM_001354825.2	c.69+35555T>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.359 AC: 54519 AN: 152058 Hom.: 10298 Cov.: 33

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.358 AC: 54541 AN: 152176 Hom.: 10299 Cov.: 33 AF XY: 0.358 AC XY: 26660 AN XY: 74412

Gnomad4 AFR AF: 0.243

Gnomad4 AMR AF: 0.383

Gnomad4 ASJ AF: 0.419

Gnomad4 EAS AF: 0.426

Gnomad4 SAS AF: 0.436

Gnomad4 FIN AF: 0.354

Gnomad4 NFE AF: 0.409

Gnomad4 OTH AF: 0.388

Alfa AF: 0.381 Hom.: 2817

Bravo AF: 0.356

Asia WGS AF: 0.421 AC: 1463 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.67
Dann	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6832344; hg19: chr4-24057536;