rs2273788

Positions:

• chr9-111586337-C-T

Variant summary

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

The NM_001146108.2(PTGR1):​c.210-172G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.252 in 151,910 control chromosomes in the GnomAD database, including 5,025 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 0.25 (5025 hom., cov: 31)
• Consequence: PTGR1 NM_001146108.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0520

Genes affected

PTGR1 (HGNC:18429): (prostaglandin reductase 1) This gene encodes an enzyme that is involved in the inactivation of the chemotactic factor, leukotriene B4. The encoded protein specifically catalyzes the NADP+ dependent conversion of leukotriene B4 to 12-oxo-leukotriene B4. A pseudogene of this gene is found on chromosome 1. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PTGR1	NM_001146108.2	c.210-172G>A		intron_variant		ENST00000407693.7	NP_001139580.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PTGR1	ENST00000407693.7	c.210-172G>A		intron_variant		1	NM_001146108.2	ENSP00000385763.2

Frequencies

GnomAD3 genomes AF: 0.252 AC: 38248 AN: 151792 Hom.: 5010 Cov.: 31

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.252 AC: 38300 AN: 151910 Hom.: 5025 Cov.: 31 AF XY: 0.247 AC XY: 18309 AN XY: 74254

Gnomad4 AFR AF: 0.315

Gnomad4 AMR AF: 0.219

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.167

Gnomad4 SAS AF: 0.217

Gnomad4 FIN AF: 0.193

Gnomad4 NFE AF: 0.246

Gnomad4 OTH AF: 0.229

Alfa AF: 0.237 Hom.: 5819

Bravo AF: 0.257

Asia WGS AF: 0.195 AC: 677 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.50

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: rs2273788; hg19: chr9-114348617;