rs16874509

chr4-23994752-G-Achr4-23994752-G-C

Variant summary

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

The NM_001330751.2(PPARGC1A):c.69+96716C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 152,078 control chromosomes in the GnomAD database, including 2,794 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 0.17 (2794 hom., cov: 32)
• Consequence: PPARGC1A NM_001330751.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.620

Genes affected

PPARGC1A (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PPARGC1A	NM_001330751.2	c.69+96716C>T		intron_variant
PPARGC1A	NM_001330752.2	c.19-109821C>T		intron_variant
PPARGC1A	NM_001354825.2	c.69+96716C>T		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26419 AN: 151960 Hom.: 2791 Cov.: 32

Gnomad AFR AF: 0.0850

Gnomad AMI AF: 0.244

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.174 AC: 26438 AN: 152078 Hom.: 2794 Cov.: 32 AF XY: 0.180 AC XY: 13386 AN XY: 74332

Gnomad4 AFR AF: 0.0849

Gnomad4 AMR AF: 0.307

Gnomad4 ASJ AF: 0.160

Gnomad4 EAS AF: 0.240

Gnomad4 SAS AF: 0.283

Gnomad4 FIN AF: 0.223

Gnomad4 NFE AF: 0.178

Gnomad4 OTH AF: 0.164

Alfa AF: 0.184 Hom.: 3679

Bravo AF: 0.175

Asia WGS AF: 0.243 AC: 842 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	4.4
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: rs16874509; hg19: chr4-23996375;