rs3766346

Variant names:

• chr1-78515594-G-A
• rs3766346
• NM_000959.4:c.799-20812G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-78515594-G-A
• chr1-78515594-G-C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 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=-0.98).
• 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 rank	MANE	Protein	UniProt
PTGFR	NM_000959.4	c.799-20812G>A		intron_variant	Intron 2 of 2	ENST00000370757.8	NP_000950.1
PTGFR	NM_001039585.2	c.869+17650G>A		intron_variant	Intron 3 of 3		NP_001034674.1
PTGFR	XM_047426085.1	c.799-20812G>A		intron_variant	Intron 2 of 2		XP_047282041.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTGFR	ENST00000370757.8	c.799-20812G>A		intron_variant	Intron 2 of 2	1	NM_000959.4	ENSP00000359793.3
PTGFR	ENST00000370758.5	c.799-20812G>A		intron_variant	Intron 3 of 3	1		ENSP00000359794.1
PTGFR	ENST00000370756.3	c.869+17650G>A		intron_variant	Intron 3 of 3	1		ENSP00000359792.3
PTGFR	ENST00000497923.5	n.870-16619G>A		intron_variant	Intron 3 of 4	3		ENSP00000432599.1

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

African (AFR) AF: 0.308 AC: 12750 AN: 41424

American (AMR) AF: 0.153 AC: 2338 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 891 AN: 3466

East Asian (EAS) AF: 0.0716 AC: 370 AN: 5168

South Asian (SAS) AF: 0.181 AC: 871 AN: 4802

European-Finnish (FIN) AF: 0.154 AC: 1620 AN: 10528

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.238 AC: 16201 AN: 67936

Other (OTH) AF: 0.196 AC: 413 AN: 2108

Alfa AF: 0.140 Hom.: 281

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
PhyloP100		1.3
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: rs3766346; hg19: chr1-78981279;