rs11751895

Variant names:

• chr6-35363327-T-C
• rs11751895
• NM_006238.5:c.-102+16177T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_006238.5(PPARD):​c.-102+16177T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.019 in 152,320 control chromosomes in the GnomAD database, including 39 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 0.019 (39 hom., cov: 32)
• Consequence: PPARD NM_006238.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.155
• Publications: 4 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]

ENSG00000297330 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.019 (2895/152320) while in subpopulation NFE AF = 0.0299 (2037/68014). AF 95% confidence interval is 0.0289. There are 39 homozygotes in GnomAd4. There are 1375 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High AC in GnomAd4 at 2895 AD gene.

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.-102+16177T>C		intron	N/A	NP_006229.1	Q03181-1
	PPARD	NM_001171818.2		c.-198+16177T>C		intron	N/A	NP_001165289.1	Q03181-1
	PPARD	NM_001171819.2		c.13+16177T>C		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.-102+16177T>C		intron	N/A	ENSP00000353916.3	Q03181-1
	PPARD	ENST00000311565.4	TSL:5	c.-198+16177T>C		intron	N/A	ENSP00000310928.4	Q03181-1
	PPARD	ENST00000875334.1		c.-102+20646T>C		intron	N/A	ENSP00000545393.1

Frequencies

GnomAD3 genomes AF: 0.0190 AC: 2897 AN: 152202 Hom.: 39 Cov.: 32

Gnomad AFR AF: 0.00567

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0199

Gnomad ASJ AF: 0.0156

Gnomad EAS AF: 0.00192

Gnomad SAS AF: 0.00849

Gnomad FIN AF: 0.0151

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0299

Gnomad OTH AF: 0.0210

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

GnomAD4 genome AF: 0.0190 AC: 2895 AN: 152320 Hom.: 39 Cov.: 32 AF XY: 0.0185 AC XY: 1375 AN XY: 74498

African (AFR) AF: 0.00565 AC: 235 AN: 41564

American (AMR) AF: 0.0199 AC: 304 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0156 AC: 54 AN: 3470

East Asian (EAS) AF: 0.00193 AC: 10 AN: 5190

South Asian (SAS) AF: 0.00849 AC: 41 AN: 4828

European-Finnish (FIN) AF: 0.0151 AC: 160 AN: 10626

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0299 AC: 2037 AN: 68014

Other (OTH) AF: 0.0203 AC: 43 AN: 2114

Alfa AF: 0.0273 Hom.: 179

Bravo AF: 0.0191

Asia WGS AF: 0.00693 AC: 24 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	1.7
DANN	Benign	0.69
PhyloP100		0.15
Mutation Taster		=100/0	polymorphism

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: rs11751895; hg19: chr6-35331104;