rs35586449

Variant names:

• chr1-78489756-A-C
• rs35586449
• ENST00000370758.5:c.-72-2916A>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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTGFR	ENST00000370758.5	c.-72-2916A>C		intron_variant	Intron 2 of 3	1		ENSP00000359794.1

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;