rs10510410

chr3-12305239-A-Cchr3-12305239-A-T

Variant summary

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

The NM_138711.6(PPARG):c.-82-7141A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.278 in 152,062 control chromosomes in the GnomAD database, including 5,984 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 0.28 (5984 hom., cov: 32)
• Consequence: PPARG NM_138711.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.129

Genes affected

PPARG (HGNC:9236): (peroxisome proliferator activated receptor gamma) This gene encodes a member of the peroxisome proliferator-activated receptor (PPAR) subfamily of nuclear receptors. PPARs form heterodimers with retinoid X receptors (RXRs) and these heterodimers regulate transcription of various genes. Three subtypes of PPARs are known: PPAR-alpha, PPAR-delta, and PPAR-gamma. The protein encoded by this gene is PPAR-gamma and is a regulator of adipocyte differentiation. Additionally, PPAR-gamma has been implicated in the pathology of numerous diseases including obesity, diabetes, atherosclerosis and cancer. Alternatively spliced transcript variants that encode different isoforms have been described. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.315 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PPARG	NM_138711.6	c.-82-7141A>C		intron_variant		ENST00000651735.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PPARG	ENST00000651735.1	c.-82-7141A>C		intron_variant			NM_138711.6	P1

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42226 AN: 151944 Hom.: 5972 Cov.: 32

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.278 AC: 42267 AN: 152062 Hom.: 5984 Cov.: 32 AF XY: 0.278 AC XY: 20693 AN XY: 74326

Gnomad4 AFR AF: 0.311

Gnomad4 AMR AF: 0.305

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.328

Gnomad4 SAS AF: 0.228

Gnomad4 FIN AF: 0.290

Gnomad4 NFE AF: 0.255

Gnomad4 OTH AF: 0.249

Alfa AF: 0.249 Hom.: 8142

Bravo AF: 0.284

Asia WGS AF: 0.235 AC: 816 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	1.2
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10510410; hg19: chr3-12346738;