dbSNP rs1047521: PTGR3:c.*3866G>T (chr18-75197550-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.59

Publications

12 publications found

Variant links:

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]

PTGR3 links:

Genome browser will be placed here

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=-0.99).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.617 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
PTGR3	NM_175907.6 link	c.*3866G>T	3_prime_UTR_variant	Exon 2 of 2	ENST00000322342.4	NP_787103.1	Q8N4Q0-1Q4G1C4
PTGR3	NM_001306093.1 link	c.*3866G>T	3_prime_UTR_variant	Exon 2 of 2		NP_001293022.1	Q8N4Q0-2
PTGR3	XM_024451166.2 link	c.*3866G>T	3_prime_UTR_variant	Exon 2 of 2		XP_024306934.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTGR3	ENST00000322342.4 link	c.*3866G>T		3_prime_UTR_variant	Exon 2 of 2	1	NM_175907.6	ENSP00000323678.3		Q8N4Q0-1

Frequencies

GnomAD3 genomes

AF:

0.560

AC:

85052

AN:

151884

Hom.:

24057

Cov.:

show subpopulations

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:

AN:

Hom.:

Cov.:

AF XY:

0.750

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.667

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.560

AC:

85139

AN:

152002

Hom.:

24096

Cov.:

AF XY:

0.561

AC XY:

41651

AN XY:

74276

show subpopulations

African (AFR)

AF:

0.623

AC:

25832

AN:

41466

American (AMR)

AF:

0.553

AC:

8446

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.659

AC:

2286

AN:

3470

East Asian (EAS)

AF:

0.432

AC:

2232

AN:

5168

South Asian (SAS)

AF:

0.456

AC:

2193

AN:

4808

European-Finnish (FIN)

AF:

0.612

AC:

6463

AN:

10552

Middle Eastern (MID)

AF:

0.656

AC:

193

AN:

294

European-Non Finnish (NFE)

AF:

0.527

AC:

35799

AN:

67952

Other (OTH)

AF:

0.609

AC:

1284

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

1962

3924

5885

7847

9809

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

720

1440

2160

2880

3600

<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:

0.537

Hom.:

65828

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

(source)

DANN

Benign

0.45

PhyloP100

-2.6

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over