rs2267665

Variant names:

• chr6-35401714-A-G
• rs2267665
• NM_006238.5:c.-101-9273A>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.-101-9273A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.851 in 152,228 control chromosomes in the GnomAD database, including 55,320 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 0.85 (55320 hom., cov: 33)
• Consequence: PPARD NM_006238.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118
• Publications: 18 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.884 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006238.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPARD	NM_006238.5	MANE Select	c.-101-9273A>G		intron	N/A	NP_006229.1	Q03181-1
	PPARD	NM_001171818.2		c.-102+4121A>G		intron	N/A	NP_001165289.1	Q03181-1
	PPARD	NM_001171819.2		c.14-18413A>G		intron	N/A	NP_001165290.1	Q03181-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPARD	ENST00000360694.8	TSL:2 MANE Select	c.-101-9273A>G		intron	N/A	ENSP00000353916.3	Q03181-1
	PPARD	ENST00000311565.4	TSL:5	c.-102+4121A>G		intron	N/A	ENSP00000310928.4	Q03181-1
	PPARD	ENST00000875334.1		c.-101-9273A>G		intron	N/A	ENSP00000545393.1

Frequencies

GnomAD3 genomes AF: 0.851 AC: 129498 AN: 152110 Hom.: 55267 Cov.: 33

Gnomad AFR AF: 0.892

Gnomad AMI AF: 0.801

Gnomad AMR AF: 0.861

Gnomad ASJ AF: 0.779

Gnomad EAS AF: 0.740

Gnomad SAS AF: 0.852

Gnomad FIN AF: 0.887

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.832

Gnomad OTH AF: 0.850

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.851 AC: 129609 AN: 152228 Hom.: 55320 Cov.: 33 AF XY: 0.852 AC XY: 63400 AN XY: 74412

African (AFR) AF: 0.892 AC: 37052 AN: 41542

American (AMR) AF: 0.861 AC: 13173 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.779 AC: 2703 AN: 3470

East Asian (EAS) AF: 0.740 AC: 3825 AN: 5168

South Asian (SAS) AF: 0.852 AC: 4113 AN: 4828

European-Finnish (FIN) AF: 0.887 AC: 9389 AN: 10586

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.832 AC: 56584 AN: 68024

Other (OTH) AF: 0.849 AC: 1797 AN: 2116

Alfa AF: 0.834 Hom.: 214632

Bravo AF: 0.853

Asia WGS AF: 0.782 AC: 2719 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.6
DANN	Benign	0.36
PhyloP100		0.12
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: rs2267665; hg19: chr6-35369491;