rs17320021

Variant names:

• chr9-111578753-T-C
• rs17320021
• NM_001146108.2:c.651+43A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001146108.2. 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
	PTGR1	NM_001146108.2	MANE Select	c.651+43A>G		intron	N/A	NP_001139580.1
	PTGR1	NM_012212.3		c.651+43A>G		intron	N/A	NP_036344.2
	PTGR1	NM_001146109.2		c.651+43A>G		intron	N/A	NP_001139581.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTGR1	ENST00000407693.7	TSL:1 MANE Select	c.651+43A>G		intron	N/A	ENSP00000385763.2
	PTGR1	ENST00000309195.9	TSL:1	c.651+43A>G		intron	N/A	ENSP00000311572.5
	PTGR1	ENST00000538962.7	TSL:2	c.651+43A>G		intron	N/A	ENSP00000440281.1

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

GnomAD2 exomes AF: 0.0583 AC: 12204 AN: 209330 AF XY: 0.0580

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 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

African (AFR) AF: 0.100 AC: 3089 AN: 30882

American (AMR) AF: 0.0359 AC: 1357 AN: 37824

Ashkenazi Jewish (ASJ) AF: 0.0832 AC: 1976 AN: 23754

East Asian (EAS) AF: 0.000103 AC: 4 AN: 39006

South Asian (SAS) AF: 0.0458 AC: 3574 AN: 77962

European-Finnish (FIN) AF: 0.0417 AC: 2151 AN: 51642

Middle Eastern (MID) AF: 0.0480 AC: 222 AN: 4622

European-Non Finnish (NFE) AF: 0.0766 AC: 81683 AN: 1066068

Other (OTH) AF: 0.0706 AC: 4059 AN: 57464

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

African (AFR) AF: 0.0993 AC: 4119 AN: 41478

American (AMR) AF: 0.0524 AC: 800 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.0862 AC: 299 AN: 3470

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5180

South Asian (SAS) AF: 0.0397 AC: 191 AN: 4814

European-Finnish (FIN) AF: 0.0352 AC: 373 AN: 10586

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0759 AC: 5162 AN: 67966

Other (OTH) AF: 0.0731 AC: 154 AN: 2108

Alfa AF: 0.0747 Hom.: 800

Bravo AF: 0.0749

Asia WGS AF: 0.0270 AC: 97 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.3
DANN	Benign	0.69
PhyloP100		-0.56
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: rs17320021; hg19: chr9-114341033;