rs1047521

Positions:

• chr18-75197550-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_175907.6(PTGR3):​c.*3866G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.56 in 152,008 control chromosomes in the GnomAD database, including 24,097 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 0.56 (24096 hom., cov: 33)
  • Exomes 𝑓: 0.67 (1 hom.)
• Consequence: PTGR3 NM_175907.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.59

Genes affected

PTGR3 (HGNC:28697): (prostaglandin reductase 3) Predicted to enable 13-prostaglandin reductase activity. Predicted to be involved in negative regulation of fat cell differentiation. Predicted to be located in peroxisome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.617 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PTGR3	NM_175907.6	c.*3866G>T		3_prime_UTR_variant	2/2	ENST00000322342.4	NP_787103.1
PTGR3	NM_001306093.1	c.*3866G>T		3_prime_UTR_variant	2/2		NP_001293022.1
PTGR3	XM_024451166.2	c.*3866G>T		3_prime_UTR_variant	2/2		XP_024306934.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PTGR3	ENST00000322342.4	c.*3866G>T		3_prime_UTR_variant	2/2	1	NM_175907.6	ENSP00000323678	P1

Frequencies

GnomAD3 genomes AF: 0.560 AC: 85052 AN: 151884 Hom.: 24057 Cov.: 33

Gnomad AFR AF: 0.623

Gnomad AMI AF: 0.451

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.455

Gnomad FIN AF: 0.612

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.605

GnomAD4 exome AF: 0.667 AC: 4 AN: 6 Hom.: 1 Cov.: 0 AF XY: 0.750 AC XY: 3 AN XY: 4

Gnomad4 NFE exome AF: 0.667

GnomAD4 genome AF: 0.560 AC: 85139 AN: 152002 Hom.: 24096 Cov.: 33 AF XY: 0.561 AC XY: 41651 AN XY: 74276

Gnomad4 AFR AF: 0.623

Gnomad4 AMR AF: 0.553

Gnomad4 ASJ AF: 0.659

Gnomad4 EAS AF: 0.432

Gnomad4 SAS AF: 0.456

Gnomad4 FIN AF: 0.612

Gnomad4 NFE AF: 0.527

Gnomad4 OTH AF: 0.609

Alfa AF: 0.533 Hom.: 21809

Bravo AF: 0.558

Asia WGS AF: 0.460 AC: 1600 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.14
DANN	Benign	0.45

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

Publications

LitVar

Other links and lift over

dbSNP: rs1047521; hg19: chr18-72909505;