rs35586449

chr1-78489756-A-C

Variant summary

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

The ENST00000370758.5(PTGFR):c.-72-2916A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0927 in 152,108 control chromosomes in the GnomAD database, including 861 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 0.093 (861 hom., cov: 32)
• Consequence: PTGFR ENST00000370758.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.345

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.131 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTGFR	ENST00000370758.5	c.-72-2916A>C		intron_variant		1		P1

Frequencies

GnomAD3 genomes AF: 0.0928 AC: 14098 AN: 151990 Hom.: 863 Cov.: 32

Gnomad AFR AF: 0.0343

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.0714

Gnomad ASJ AF: 0.0994

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.0831

Gnomad FIN AF: 0.0882

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.0808

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0927 AC: 14103 AN: 152108 Hom.: 861 Cov.: 32 AF XY: 0.0918 AC XY: 6827 AN XY: 74376

Gnomad4 AFR AF: 0.0344

Gnomad4 AMR AF: 0.0713

Gnomad4 ASJ AF: 0.0994

Gnomad4 EAS AF: 0.112

Gnomad4 SAS AF: 0.0831

Gnomad4 FIN AF: 0.0882

Gnomad4 NFE AF: 0.133

Gnomad4 OTH AF: 0.0809

Alfa AF: 0.118 Hom.: 156

Bravo AF: 0.0882

Asia WGS AF: 0.0890 AC: 313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	5.9
Dann	Benign	0.77

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: rs35586449; hg19: chr1-78955441;