rs9794

Variant names:

• chr6-35428018-G-A
• rs9794
• NM_006238.5:c.*1939G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-35428018-G-A
• chr6-35428018-G-C
• chr6-35428018-G-T

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.*1939G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0133 in 152,684 control chromosomes in the GnomAD database, including 13 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 0.013 (13 hom., cov: 32)
  • Exomes 𝑓: 0.021 (0 hom.)
• Consequence: PPARD NM_006238.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.91
• Publications: 35 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=-0.83).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0133 (2025/152254) while in subpopulation AFR AF = 0.0248 (1029/41552). AF 95% confidence interval is 0.0235. There are 13 homozygotes in GnomAd4. There are 975 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High AC in GnomAd4 at 2025 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.*1939G>A		3_prime_UTR	Exon 8 of 8	NP_006229.1	Q03181-1
	PPARD	NM_001171818.2		c.*1939G>A		3_prime_UTR	Exon 9 of 9	NP_001165289.1	Q03181-1
	PPARD	NM_001171819.2		c.*1939G>A		3_prime_UTR	Exon 7 of 7	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.*1939G>A		3_prime_UTR	Exon 8 of 8	ENSP00000353916.3	Q03181-1
	PPARD	ENST00000311565.4	TSL:5	c.*1939G>A		3_prime_UTR	Exon 9 of 9	ENSP00000310928.4	Q03181-1
	PPARD	ENST00000875334.1		c.*1939G>A		3_prime_UTR	Exon 7 of 7	ENSP00000545393.1

Frequencies

GnomAD3 genomes AF: 0.0133 AC: 2020 AN: 152136 Hom.: 13 Cov.: 32

Gnomad AFR AF: 0.0247

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0140

Gnomad ASJ AF: 0.0176

Gnomad EAS AF: 0.000775

Gnomad SAS AF: 0.0139

Gnomad FIN AF: 0.00839

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.00775

Gnomad OTH AF: 0.0119

GnomAD4 exome AF: 0.0209 AC: 9 AN: 430 Hom.: 0 Cov.: 0 AF XY: 0.0222 AC XY: 6 AN XY: 270

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.500 AC: 1 AN: 2

European-Finnish (FIN) AF: 0.0151 AC: 6 AN: 398

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.0833 AC: 2 AN: 24

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.0133 AC: 2025 AN: 152254 Hom.: 13 Cov.: 32 AF XY: 0.0131 AC XY: 975 AN XY: 74432

African (AFR) AF: 0.0248 AC: 1029 AN: 41552

American (AMR) AF: 0.0140 AC: 214 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0176 AC: 61 AN: 3470

East Asian (EAS) AF: 0.000777 AC: 4 AN: 5150

South Asian (SAS) AF: 0.0139 AC: 67 AN: 4824

European-Finnish (FIN) AF: 0.00839 AC: 89 AN: 10610

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.00775 AC: 527 AN: 68020

Other (OTH) AF: 0.0118 AC: 25 AN: 2116

Alfa AF: 0.00217 Hom.: 2584

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.027
DANN	Benign	0.93
PhyloP100		-1.9
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: rs9794; hg19: chr6-35395795;