rs3766346

chr1-78515594-G-Achr1-78515594-G-C

Variant summary

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

The NM_000959.4(PTGFR):c.799-20812G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 151,916 control chromosomes in the GnomAD database, including 4,483 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 0.23 (4483 hom., cov: 32)
• Consequence: PTGFR NM_000959.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.34

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTGFR	NM_000959.4	c.799-20812G>A		intron_variant		ENST00000370757.8
PTGFR	NM_001039585.2	c.869+17650G>A		intron_variant
PTGFR	XM_047426085.1	c.799-20812G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTGFR	ENST00000370757.8	c.799-20812G>A		intron_variant		1	NM_000959.4	P1
PTGFR	ENST00000370756.3	c.869+17650G>A		intron_variant		1
PTGFR	ENST00000370758.5	c.799-20812G>A		intron_variant		1		P1
PTGFR	ENST00000497923.5	c.870-16619G>A		intron_variant, NMD_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35623 AN: 151798 Hom.: 4478 Cov.: 32

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.172

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.0716

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.235 AC: 35656 AN: 151916 Hom.: 4483 Cov.: 32 AF XY: 0.227 AC XY: 16819 AN XY: 74238

Gnomad4 AFR AF: 0.308

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.257

Gnomad4 EAS AF: 0.0716

Gnomad4 SAS AF: 0.181

Gnomad4 FIN AF: 0.154

Gnomad4 NFE AF: 0.238

Gnomad4 OTH AF: 0.196

Alfa AF: 0.130 Hom.: 237

Bravo AF: 0.237

Asia WGS AF: 0.129 AC: 450 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	7.1
Dann	Benign	0.46

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: rs3766346; hg19: chr1-78981279;