rs4684847

Variant summary

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

The NM_138711.6(PPARG):​c.-9+32385C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0892 in 152,140 control chromosomes in the GnomAD database, including 766 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 0.089 ( 766 hom., cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

PPARG
NM_138711.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.155
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.124 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PPARGNM_138711.6 linkuse as main transcriptc.-9+32385C>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.-9+32385C>T intron_variant NM_138711.6 ENSP00000498313 P1

Frequencies

GnomAD3 genomes
AF:
0.0893
AC:
13578
AN:
152022
Hom.:
763
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0214
Gnomad AMI
AF:
0.0285
Gnomad AMR
AF:
0.0841
Gnomad ASJ
AF:
0.0578
Gnomad EAS
AF:
0.0407
Gnomad SAS
AF:
0.123
Gnomad FIN
AF:
0.156
Gnomad MID
AF:
0.0633
Gnomad NFE
AF:
0.126
Gnomad OTH
AF:
0.0633
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
2
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
2
Gnomad4 NFE exome
AF:
0.00
GnomAD4 genome
AF:
0.0892
AC:
13575
AN:
152140
Hom.:
766
Cov.:
32
AF XY:
0.0898
AC XY:
6674
AN XY:
74354
show subpopulations
Gnomad4 AFR
AF:
0.0213
Gnomad4 AMR
AF:
0.0839
Gnomad4 ASJ
AF:
0.0578
Gnomad4 EAS
AF:
0.0406
Gnomad4 SAS
AF:
0.124
Gnomad4 FIN
AF:
0.156
Gnomad4 NFE
AF:
0.126
Gnomad4 OTH
AF:
0.0626
Alfa
AF:
0.109
Hom.:
965
Bravo
AF:
0.0802
Asia WGS
AF:
0.0570
AC:
198
AN:
3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
8.7
DANN
Benign
0.77

Splicing

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: rs4684847; hg19: chr3-12386337; API