chr1-78490747-T-C

Variant names:

• chr1-78490747-T-C
• rs3753380
• ENST00000370758.5:c.-72-1925T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000370758.5(PTGFR):​c.-72-1925T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.775 in 152,210 control chromosomes in the GnomAD database, including 46,665 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 0.78 (46665 hom., cov: 33)
• Consequence: PTGFR ENST00000370758.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.817
• Publications: 22 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.94 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTGFR	NM_000959.4	c.-562T>C		upstream_gene_variant		ENST00000370757.8	NP_000950.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTGFR	ENST00000370758.5	c.-72-1925T>C		intron_variant	Intron 2 of 3	1		ENSP00000359794.1
PTGFR	ENST00000370757.8	c.-562T>C		upstream_gene_variant		1	NM_000959.4	ENSP00000359793.3

Frequencies

GnomAD3 genomes AF: 0.775 AC: 117867 AN: 152092 Hom.: 46614 Cov.: 33

Gnomad AFR AF: 0.948

Gnomad AMI AF: 0.819

Gnomad AMR AF: 0.768

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.715

Gnomad SAS AF: 0.745

Gnomad FIN AF: 0.627

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.704

Gnomad OTH AF: 0.761

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

GnomAD4 genome AF: 0.775 AC: 117971 AN: 152210 Hom.: 46665 Cov.: 33 AF XY: 0.772 AC XY: 57452 AN XY: 74384

African (AFR) AF: 0.948 AC: 39399 AN: 41574

American (AMR) AF: 0.768 AC: 11739 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.709 AC: 2462 AN: 3472

East Asian (EAS) AF: 0.715 AC: 3698 AN: 5172

South Asian (SAS) AF: 0.743 AC: 3584 AN: 4824

European-Finnish (FIN) AF: 0.627 AC: 6621 AN: 10556

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.704 AC: 47901 AN: 67996

Other (OTH) AF: 0.758 AC: 1603 AN: 2116

Alfa AF: 0.736 Hom.: 94181

Bravo AF: 0.795

Asia WGS AF: 0.717 AC: 2495 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.5
DANN	Benign	0.27
PhyloP100		-0.82
PromoterAI		0.015	Neutral
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3753380; hg19: chr1-78956432;