rs1822825

Variant names:

• chr3-12408464-G-A
• rs1822825
• NM_138711.6:c.729+2383G>A

Your query was ambiguous. Multiple possible variants found:

• chr3-12408464-G-A
• chr3-12408464-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_138711.6(PPARG):​c.729+2383G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.599 in 151,772 control chromosomes in the GnomAD database, including 28,674 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 0.60 (28674 hom., cov: 31)
• Consequence: PPARG NM_138711.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800
• Publications: 13 publications found

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]

PPARG Gene-Disease associations (from GenCC):

• PPARG-related familial partial lipodystrophy

  Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet, Ambry Genetics, G2P, Genomics England PanelApp
• Berardinelli-Seip congenital lipodystrophy

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.795 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PPARG	NM_138711.6	c.729+2383G>A		intron_variant	Intron 6 of 7	ENST00000651735.1	NP_619725.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPARG	ENST00000651735.1	c.729+2383G>A		intron_variant	Intron 6 of 7		NM_138711.6	ENSP00000498313.1

Frequencies

GnomAD3 genomes AF: 0.599 AC: 90859 AN: 151654 Hom.: 28622 Cov.: 31

Gnomad AFR AF: 0.802

Gnomad AMI AF: 0.752

Gnomad AMR AF: 0.572

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.427

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.580

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.600

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

GnomAD4 genome AF: 0.599 AC: 90969 AN: 151772 Hom.: 28674 Cov.: 31 AF XY: 0.595 AC XY: 44108 AN XY: 74090

African (AFR) AF: 0.802 AC: 33207 AN: 41414

American (AMR) AF: 0.572 AC: 8714 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.621 AC: 2156 AN: 3472

East Asian (EAS) AF: 0.428 AC: 2207 AN: 5158

South Asian (SAS) AF: 0.329 AC: 1583 AN: 4816

European-Finnish (FIN) AF: 0.539 AC: 5637 AN: 10458

Middle Eastern (MID) AF: 0.582 AC: 170 AN: 292

European-Non Finnish (NFE) AF: 0.521 AC: 35348 AN: 67906

Other (OTH) AF: 0.601 AC: 1263 AN: 2102

Alfa AF: 0.556 Hom.: 30543

Bravo AF: 0.618

Asia WGS AF: 0.449 AC: 1562 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.60
DANN	Benign	0.59
PhyloP100		-0.080
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1822825; hg19: chr3-12449963;