1-78489470-C-T

Variant names:

• chr1-78489470-C-T
• rs12093097
• ENST00000370758.5:c.-72-3202C>T

Variant summary

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

The ENST00000370758.5(PTGFR):​c.-72-3202C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.247 in 152,066 control chromosomes in the GnomAD database, including 6,934 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 0.25 (6934 hom., cov: 32)
• Consequence: PTGFR ENST00000370758.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.632

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.513 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.-72-3202C>T		intron_variant	Intron 2 of 3	1		ENSP00000359794.1

Frequencies

GnomAD3 genomes AF: 0.247 AC: 37547 AN: 151948 Hom.: 6913 Cov.: 32

Gnomad AFR AF: 0.518

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.0782

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.0998

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.247 AC: 37605 AN: 152066 Hom.: 6934 Cov.: 32 AF XY: 0.242 AC XY: 17990 AN XY: 74340

Gnomad4 AFR AF: 0.519

Gnomad4 AMR AF: 0.158

Gnomad4 ASJ AF: 0.191

Gnomad4 EAS AF: 0.0780

Gnomad4 SAS AF: 0.130

Gnomad4 FIN AF: 0.0998

Gnomad4 NFE AF: 0.149

Gnomad4 OTH AF: 0.246

Alfa AF: 0.0867 Hom.: 144

Bravo AF: 0.265

Asia WGS AF: 0.122 AC: 425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.39

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: rs12093097; hg19: chr1-78955155;