rs9462082

Variant summary

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

The NM_006238.5(PPARD):​c.131-1863A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.868 in 152,266 control chromosomes in the GnomAD database, including 57,557 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 0.87 ( 57557 hom., cov: 33)

Consequence

PPARD
NM_006238.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.666
Variant links:
Genes affected
PPARD (HGNC:9235): (peroxisome proliferator activated receptor delta) This gene encodes a member of the peroxisome proliferator-activated receptor (PPAR) family. The encoded protein is thought to function as an integrator of transcriptional repression and nuclear receptor signaling. It may inhibit the ligand-induced transcriptional activity of peroxisome proliferator activated receptors alpha and gamma, though evidence for this effect is inconsistent. Expression of this gene in colorectal cancer cells may be variable but is typically relatively low. Knockout studies in mice suggested a role for this protein in myelination of the corpus callosum, lipid metabolism, differentiation, and epidermal cell proliferation. Alternative splicing results in multiple transcript variants encoding distinct protein isoforms. [provided by RefSeq, Aug 2017]

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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 (AFR) allele frequency at 95% confidence interval = 0.913 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PPARDNM_006238.5 linkuse as main transcriptc.131-1863A>G intron_variant ENST00000360694.8 NP_006229.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PPARDENST00000360694.8 linkuse as main transcriptc.131-1863A>G intron_variant 2 NM_006238.5 ENSP00000353916 P1Q03181-1

Frequencies

GnomAD3 genomes
AF:
0.868
AC:
132046
AN:
152148
Hom.:
57496
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.920
Gnomad AMI
AF:
0.814
Gnomad AMR
AF:
0.864
Gnomad ASJ
AF:
0.775
Gnomad EAS
AF:
0.747
Gnomad SAS
AF:
0.862
Gnomad FIN
AF:
0.916
Gnomad MID
AF:
0.839
Gnomad NFE
AF:
0.845
Gnomad OTH
AF:
0.857
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.868
AC:
132165
AN:
152266
Hom.:
57557
Cov.:
33
AF XY:
0.869
AC XY:
64710
AN XY:
74460
show subpopulations
Gnomad4 AFR
AF:
0.920
Gnomad4 AMR
AF:
0.864
Gnomad4 ASJ
AF:
0.775
Gnomad4 EAS
AF:
0.747
Gnomad4 SAS
AF:
0.862
Gnomad4 FIN
AF:
0.916
Gnomad4 NFE
AF:
0.845
Gnomad4 OTH
AF:
0.857
Alfa
AF:
0.846
Hom.:
55274
Bravo
AF:
0.868
Asia WGS
AF:
0.790
AC:
2745
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
1.7
DANN
Benign
0.56

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: rs9462082; hg19: chr6-35386041; API