rs9462082

Variant names:

• chr6-35418264-A-G
• rs9462082
• NM_006238.5:c.131-1863A>G

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.666
• Publications: 17 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PPARD	NM_006238.5	c.131-1863A>G		intron_variant	Intron 3 of 7	ENST00000360694.8	NP_006229.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPARD	ENST00000360694.8	c.131-1863A>G		intron_variant	Intron 3 of 7	2	NM_006238.5	ENSP00000353916.3

Frequencies

GnomAD3 genomes AF: 0.868 AC: 132046 AN: 152148 Hom.: 57496 Cov.: 33

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

African (AFR) AF: 0.920 AC: 38244 AN: 41556

American (AMR) AF: 0.864 AC: 13228 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.775 AC: 2686 AN: 3468

East Asian (EAS) AF: 0.747 AC: 3857 AN: 5162

South Asian (SAS) AF: 0.862 AC: 4161 AN: 4828

European-Finnish (FIN) AF: 0.916 AC: 9721 AN: 10610

Middle Eastern (MID) AF: 0.844 AC: 248 AN: 294

European-Non Finnish (NFE) AF: 0.845 AC: 57465 AN: 68010

Other (OTH) AF: 0.857 AC: 1813 AN: 2116

Alfa AF: 0.851 Hom.: 72875

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
PhyloP100		-0.67
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: rs9462082; hg19: chr6-35386041;