Genetic Variant NM_000959.4:c.*217A>G (chr1-78536904-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_000959.4(PTGFR):c.*217A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 533,852 control chromosomes in the GnomAD database, including 7,084 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 0.15 ( 1869 hom., cov: 32)

Exomes 𝑓: 0.16 ( 5215 hom. )

Consequence

PTGFR
NM_000959.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.405

Publications

17 publications found

Variant links:

Genes affected

PTGFR (HGNC:9600): (prostaglandin F receptor) The protein encoded by this gene is member of the G-protein coupled receptor family. This protein is a receptor for prostaglandin F2-alpha (PGF2-alpha), which is known to be a potent luteolytic agent, and may also be involved in modulating intraocular pressure and smooth muscle contraction in uterus. Knockout studies in mice suggest that the interaction of PGF2-alpha with this receptor may initiate parturition in ovarian luteal cells and thus induce luteolysis. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

PTGFR 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=-0.92).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
PTGFR	NM_000959.4 link	c.*217A>G	3_prime_UTR_variant	Exon 3 of 3	ENST00000370757.8	NP_000950.1	P43088-1
PTGFR	NM_001039585.2 link	c.*474A>G	3_prime_UTR_variant	Exon 4 of 4		NP_001034674.1	P43088-2
PTGFR	XM_047426085.1 link	c.*217A>G	3_prime_UTR_variant	Exon 3 of 3		XP_047282041.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTGFR	ENST00000370757.8 link	c.*217A>G		3_prime_UTR_variant	Exon 3 of 3	1	NM_000959.4	ENSP00000359793.3		P43088-1

Frequencies

GnomAD3 genomes

AF:

0.152

AC:

23133

AN:

152006

Hom.:

1864

Cov.:

show subpopulations

Gnomad AFR

AF:

0.152

Gnomad AMI

AF:

0.133

Gnomad AMR

AF:

0.101

Gnomad ASJ

AF:

0.116

Gnomad EAS

AF:

0.0164

Gnomad SAS

AF:

0.138

Gnomad FIN

AF:

0.113

Gnomad MID

AF:

0.108

Gnomad NFE

AF:

0.184

Gnomad OTH

AF:

0.132

GnomAD4 exome

AF:

0.157

AC:

59779

AN:

381728

Hom.:

5215

Cov.:

AF XY:

0.156

AC XY:

31066

AN XY:

198976

show subpopulations

African (AFR)

AF:

0.146

AC:

1431

AN:

9816

American (AMR)

AF:

0.0889

AC:

1036

AN:

11660

Ashkenazi Jewish (ASJ)

AF:

0.121

AC:

1416

AN:

11718

East Asian (EAS)

AF:

0.0119

AC:

300

AN:

25278

South Asian (SAS)

AF:

0.138

AC:

4249

AN:

30890

European-Finnish (FIN)

AF:

0.137

AC:

3333

AN:

24412

Middle Eastern (MID)

AF:

0.135

AC:

226

AN:

1680

European-Non Finnish (NFE)

AF:

0.182

AC:

44476

AN:

243916

Other (OTH)

AF:

0.148

AC:

3312

AN:

22358

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

2309

4618

6927

9236

11545

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

374

748

1122

1496

1870

<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:

0.152

AC:

23164

AN:

152124

Hom.:

1869

Cov.:

AF XY:

0.148

AC XY:

10996

AN XY:

74364

show subpopulations

African (AFR)

AF:

0.152

AC:

6318

AN:

41502

American (AMR)

AF:

0.101

AC:

1535

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.116

AC:

403

AN:

3466

East Asian (EAS)

AF:

0.0164

AC:

AN:

5174

South Asian (SAS)

AF:

0.139

AC:

670

AN:

4828

European-Finnish (FIN)

AF:

0.113

AC:

1198

AN:

10604

Middle Eastern (MID)

AF:

0.112

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.184

AC:

12524

AN:

67966

Other (OTH)

AF:

0.131

AC:

277

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1014

2028

3041

4055

5069

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

268

536

804

1072

1340

<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:

0.175

Hom.:

607

Bravo

AF:

0.148

Asia WGS

AF:

0.0790

AC:

274

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

6.9

(source)

DANN

Benign

0.58

PhyloP100

0.41

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