chr6-35420702-A-G

Variant names:

• chr6-35420702-A-G
• rs2076169
• NM_006238.5:c.285+421A>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.285+421A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.08 in 152,232 control chromosomes in the GnomAD database, including 693 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 0.080 (693 hom., cov: 32)
• Consequence: PPARD NM_006238.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.758
• Publications: 20 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 (EAS) allele frequency at 95% confidence interval = 0.235 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPARD	NM_006238.5	MANE Select	c.285+421A>G		intron	N/A	NP_006229.1
	PPARD	NM_001171818.2		c.285+421A>G		intron	N/A	NP_001165289.1
	PPARD	NM_001171819.2		c.168+421A>G		intron	N/A	NP_001165290.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPARD	ENST00000360694.8	TSL:2 MANE Select	c.285+421A>G		intron	N/A	ENSP00000353916.3
	PPARD	ENST00000311565.4	TSL:5	c.285+421A>G		intron	N/A	ENSP00000310928.4
	PPARD	ENST00000448077.6	TSL:2	c.168+421A>G		intron	N/A	ENSP00000414372.2

Frequencies

GnomAD3 genomes AF: 0.0801 AC: 12184 AN: 152114 Hom.: 692 Cov.: 32

Gnomad AFR AF: 0.0202

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.0904

Gnomad ASJ AF: 0.0900

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.0698

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0998

Gnomad OTH AF: 0.0799

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

GnomAD4 genome AF: 0.0800 AC: 12185 AN: 152232 Hom.: 693 Cov.: 32 AF XY: 0.0808 AC XY: 6016 AN XY: 74436

African (AFR) AF: 0.0201 AC: 837 AN: 41560

American (AMR) AF: 0.0904 AC: 1383 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0900 AC: 312 AN: 3468

East Asian (EAS) AF: 0.246 AC: 1275 AN: 5174

South Asian (SAS) AF: 0.123 AC: 592 AN: 4820

European-Finnish (FIN) AF: 0.0698 AC: 740 AN: 10598

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0998 AC: 6786 AN: 67994

Other (OTH) AF: 0.0814 AC: 172 AN: 2112

Alfa AF: 0.0898 Hom.: 1272

Bravo AF: 0.0768

Asia WGS AF: 0.180 AC: 625 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	0.23
DANN	Benign	0.76
PhyloP100		-0.76
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: rs2076169; hg19: chr6-35388479;