rs7682906

chr4-23986441-C-A

Variant summary

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

The NM_001330751.2(PPARGC1A):c.70-101510G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.588 in 151,850 control chromosomes in the GnomAD database, including 27,032 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 0.59 (27032 hom., cov: 33)
• Consequence: PPARGC1A NM_001330751.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49

Genes affected

PPARGC1A (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.678 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PPARGC1A	NM_001330751.2	c.70-101510G>T		intron_variant
PPARGC1A	NM_001330752.2	c.19-101510G>T		intron_variant
PPARGC1A	NM_001354825.2	c.70-101510G>T		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.588 AC: 89234 AN: 151730 Hom.: 27019 Cov.: 33

Gnomad AFR AF: 0.685

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.566

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.599

Gnomad OTH AF: 0.553

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

GnomAD4 genome AF: 0.588 AC: 89277 AN: 151850 Hom.: 27032 Cov.: 33 AF XY: 0.580 AC XY: 43017 AN XY: 74228

Gnomad4 AFR AF: 0.685

Gnomad4 AMR AF: 0.437

Gnomad4 ASJ AF: 0.566

Gnomad4 EAS AF: 0.316

Gnomad4 SAS AF: 0.416

Gnomad4 FIN AF: 0.587

Gnomad4 NFE AF: 0.599

Gnomad4 OTH AF: 0.548

Alfa AF: 0.589 Hom.: 7923

Bravo AF: 0.580

Asia WGS AF: 0.361 AC: 1259 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	0.094
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7682906; hg19: chr4-23988064;