chr3-12430372-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_138711.6(PPARG):​c.1181-3526C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.449 in 151,996 control chromosomes in the GnomAD database, including 15,437 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 0.45 ( 15437 hom., cov: 32)

Consequence

PPARG
NM_138711.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.360
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PPARGNM_138711.6 linkuse as main transcriptc.1181-3526C>T intron_variant ENST00000651735.1 NP_619725.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PPARGENST00000651735.1 linkuse as main transcriptc.1181-3526C>T intron_variant NM_138711.6 ENSP00000498313 P1

Frequencies

GnomAD3 genomes
AF:
0.449
AC:
68219
AN:
151878
Hom.:
15426
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.434
Gnomad AMI
AF:
0.545
Gnomad AMR
AF:
0.406
Gnomad ASJ
AF:
0.479
Gnomad EAS
AF:
0.427
Gnomad SAS
AF:
0.216
Gnomad FIN
AF:
0.472
Gnomad MID
AF:
0.421
Gnomad NFE
AF:
0.480
Gnomad OTH
AF:
0.459
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.449
AC:
68267
AN:
151996
Hom.:
15437
Cov.:
32
AF XY:
0.444
AC XY:
32947
AN XY:
74270
show subpopulations
Gnomad4 AFR
AF:
0.434
Gnomad4 AMR
AF:
0.405
Gnomad4 ASJ
AF:
0.479
Gnomad4 EAS
AF:
0.428
Gnomad4 SAS
AF:
0.215
Gnomad4 FIN
AF:
0.472
Gnomad4 NFE
AF:
0.480
Gnomad4 OTH
AF:
0.459
Alfa
AF:
0.472
Hom.:
16565
Bravo
AF:
0.448
Asia WGS
AF:
0.370
AC:
1286
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
4.4
DANN
Benign
0.71

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1152002; hg19: chr3-12471871; API