Genetic Variant PTGR1:c.651+43A>G (chr9-111578753-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.565

Publications

5 publications found

Variant links:

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]

PTGR1 links:

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ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTGR1	NM_001146108.2 link	c.651+43A>G		intron_variant	Intron 7 of 9	ENST00000407693.7	NP_001139580.1	Q14914-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTGR1	ENST00000407693.7 link	c.651+43A>G		intron_variant	Intron 7 of 9	1	NM_001146108.2	ENSP00000385763.2		Q14914-1

Frequencies

GnomAD3 genomes

AF:

0.0733

AC:

11143

AN:

151946

Hom.:

478

Cov.:

show subpopulations

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

show subpopulations

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.:

AF XY:

0.0699

AC XY:

48280

AN XY:

690632

show subpopulations

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:

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

4395

8791

13186

17582

21977

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2978

5956

8934

11912

14890

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0734

AC:

11163

AN:

152064

Hom.:

478

Cov.:

AF XY:

0.0700

AC XY:

5204

AN XY:

74336

show subpopulations

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:

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:

AN:

294

European-Non Finnish (NFE)

AF:

0.0759

AC:

5162

AN:

67966

Other (OTH)

AF:

0.0731

AC:

154

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

519

1037

1556

2074

2593

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

126

252

378

504

630

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0747

Hom.:

800

Bravo

AF:

0.0749

Asia WGS

AF:

0.0270

AC:

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

(source)

DANN

Benign

0.69

PhyloP100

-0.56

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over