rs17320021

Positions:

• chr9-111578753-T-C

Variant summary

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

The NM_001146108.2(PTGR1):​c.651+43A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0709 in 1,541,288 control chromosomes in the GnomAD database, including 4,242 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 0.073 (478 hom., cov: 30)
  • Exomes 𝑓: 0.071 (3764 hom.)
• Consequence: PTGR1 NM_001146108.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.565

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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0968 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTGR1	NM_001146108.2	c.651+43A>G		intron_variant		ENST00000407693.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTGR1	ENST00000407693.7	c.651+43A>G		intron_variant		1	NM_001146108.2	P1

Frequencies

GnomAD3 genomes AF: 0.0733 AC: 11143 AN: 151946 Hom.: 478 Cov.: 30

Gnomad AFR AF: 0.0991

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.0525

Gnomad ASJ AF: 0.0862

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0401

Gnomad FIN AF: 0.0352

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0759

Gnomad OTH AF: 0.0738

GnomAD3 exomes AF: 0.0583 AC: 12204 AN: 209330 Hom.: 434 AF XY: 0.0580 AC XY: 6523 AN XY: 112550

Gnomad AFR exome AF: 0.103

Gnomad AMR exome AF: 0.0336

Gnomad ASJ exome AF: 0.0887

Gnomad EAS exome AF: 0.000367

Gnomad SAS exome AF: 0.0451

Gnomad FIN exome AF: 0.0370

Gnomad NFE exome AF: 0.0737

Gnomad OTH exome AF: 0.0599

GnomAD4 exome AF: 0.0706 AC: 98115 AN: 1389224 Hom.: 3764 Cov.: 25 AF XY: 0.0699 AC XY: 48280 AN XY: 690632

Gnomad4 AFR exome AF: 0.100

Gnomad4 AMR exome AF: 0.0359

Gnomad4 ASJ exome AF: 0.0832

Gnomad4 EAS exome AF: 0.000103

Gnomad4 SAS exome AF: 0.0458

Gnomad4 FIN exome AF: 0.0417

Gnomad4 NFE exome AF: 0.0766

Gnomad4 OTH exome AF: 0.0706

GnomAD4 genome AF: 0.0734 AC: 11163 AN: 152064 Hom.: 478 Cov.: 30 AF XY: 0.0700 AC XY: 5204 AN XY: 74336

Gnomad4 AFR AF: 0.0993

Gnomad4 AMR AF: 0.0524

Gnomad4 ASJ AF: 0.0862

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0397

Gnomad4 FIN AF: 0.0352

Gnomad4 NFE AF: 0.0759

Gnomad4 OTH AF: 0.0731

Alfa AF: 0.0739 Hom.: 629

Bravo AF: 0.0749

Asia WGS AF: 0.0270 AC: 97 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.3
DANN	Benign	0.69

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: rs17320021; hg19: chr9-114341033;