rs4697055

Positions:

• chr4-24265713-A-G
• chr4-24265713-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.-164-7446T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 152,020 control chromosomes in the GnomAD database, including 7,806 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 0.30 (7806 hom., cov: 31)
• Consequence: PPARGC1A NM_001330751.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.389

Genes affected

PPARGC1A (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PPARGC1A	NM_001330751.2	c.-164-7446T>C		intron_variant
PPARGC1A	NM_001330752.2	c.-47-7446T>C		intron_variant
PPARGC1A	NM_001354825.2	c.-99-174078T>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45942 AN: 151900 Hom.: 7805 Cov.: 31

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.258

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.302 AC: 45979 AN: 152020 Hom.: 7806 Cov.: 31 AF XY: 0.306 AC XY: 22748 AN XY: 74296

Gnomad4 AFR AF: 0.458

Gnomad4 AMR AF: 0.286

Gnomad4 ASJ AF: 0.239

Gnomad4 EAS AF: 0.461

Gnomad4 SAS AF: 0.291

Gnomad4 FIN AF: 0.254

Gnomad4 NFE AF: 0.214

Gnomad4 OTH AF: 0.283

Alfa AF: 0.237 Hom.: 2205

Bravo AF: 0.313

Asia WGS AF: 0.333 AC: 1155 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.7
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4697055; hg19: chr4-24267336;