rs6007662

Variant summary

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

The NM_005036.6(PPARA):​c.711+5134A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.353 in 151,898 control chromosomes in the GnomAD database, including 11,936 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 0.35 ( 11936 hom., cov: 31)

Consequence

PPARA
NM_005036.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.908
Variant links:
Genes affected
PPARA (HGNC:9232): (peroxisome proliferator activated receptor alpha) Peroxisome proliferators include hypolipidemic drugs, herbicides, leukotriene antagonists, and plasticizers; this term arises because they induce an increase in the size and number of peroxisomes. Peroxisomes are subcellular organelles found in plants and animals that contain enzymes for respiration and for cholesterol and lipid metabolism. The action of peroxisome proliferators is thought to be mediated via specific receptors, called PPARs, which belong to the steroid hormone receptor superfamily. PPARs affect the expression of target genes involved in cell proliferation, cell differentiation and in immune and inflammation responses. Three closely related subtypes (alpha, beta/delta, and gamma) have been identified. This gene encodes the subtype PPAR-alpha, which is a nuclear transcription factor. Multiple alternatively spliced transcript variants have been described for this gene, although the full-length nature of only two has been determined. [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=-0.98).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PPARANM_005036.6 linkuse as main transcriptc.711+5134A>G intron_variant ENST00000407236.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PPARAENST00000407236.6 linkuse as main transcriptc.711+5134A>G intron_variant 1 NM_005036.6 P1Q07869-1
PPARAENST00000402126.1 linkuse as main transcriptc.711+5134A>G intron_variant 1 P1Q07869-1

Frequencies

GnomAD3 genomes
AF:
0.353
AC:
53613
AN:
151780
Hom.:
11910
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.633
Gnomad AMI
AF:
0.260
Gnomad AMR
AF:
0.260
Gnomad ASJ
AF:
0.231
Gnomad EAS
AF:
0.149
Gnomad SAS
AF:
0.106
Gnomad FIN
AF:
0.300
Gnomad MID
AF:
0.247
Gnomad NFE
AF:
0.255
Gnomad OTH
AF:
0.307
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.353
AC:
53684
AN:
151898
Hom.:
11936
Cov.:
31
AF XY:
0.349
AC XY:
25923
AN XY:
74262
show subpopulations
Gnomad4 AFR
AF:
0.633
Gnomad4 AMR
AF:
0.260
Gnomad4 ASJ
AF:
0.231
Gnomad4 EAS
AF:
0.149
Gnomad4 SAS
AF:
0.105
Gnomad4 FIN
AF:
0.300
Gnomad4 NFE
AF:
0.255
Gnomad4 OTH
AF:
0.303
Alfa
AF:
0.261
Hom.:
7493
Bravo
AF:
0.365
Asia WGS
AF:
0.140
AC:
491
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
0.078
DANN
Benign
0.23
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
0.97

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: rs6007662; hg19: chr22-46621045; API