NM_000959.4:c.799-2822G>A

Variant names:

• chr1-78533584-G-A
• rs3766335
• NM_000959.4:c.799-2822G>A

Variant summary

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

The NM_000959.4(PTGFR):​c.799-2822G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 152,104 control chromosomes in the GnomAD database, including 2,201 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 0.16 (2201 hom., cov: 32)
• Consequence: PTGFR NM_000959.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.244
• Publications: 3 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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTGFR	NM_000959.4	c.799-2822G>A		intron_variant	Intron 2 of 2	ENST00000370757.8	NP_000950.1
PTGFR	NM_001039585.2	c.870-2822G>A		intron_variant	Intron 3 of 3		NP_001034674.1
PTGFR	XM_047426085.1	c.799-2822G>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.799-2822G>A		intron_variant	Intron 2 of 2	1	NM_000959.4	ENSP00000359793.3
PTGFR	ENST00000370758.5	c.799-2822G>A		intron_variant	Intron 3 of 3	1		ENSP00000359794.1
PTGFR	ENST00000370756.3	c.870-2822G>A		intron_variant	Intron 3 of 3	1		ENSP00000359792.3
PTGFR	ENST00000497923.5	n.*116+1231G>A		intron_variant	Intron 4 of 4	3		ENSP00000432599.1

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24737 AN: 151986 Hom.: 2200 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.0599

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.163 AC: 24741 AN: 152104 Hom.: 2201 Cov.: 32 AF XY: 0.156 AC XY: 11631 AN XY: 74350

African (AFR) AF: 0.114 AC: 4721 AN: 41508

American (AMR) AF: 0.117 AC: 1788 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 731 AN: 3468

East Asian (EAS) AF: 0.0598 AC: 310 AN: 5184

South Asian (SAS) AF: 0.161 AC: 776 AN: 4822

European-Finnish (FIN) AF: 0.113 AC: 1193 AN: 10600

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.216 AC: 14639 AN: 67928

Other (OTH) AF: 0.145 AC: 307 AN: 2112

Alfa AF: 0.196 Hom.: 5118

Bravo AF: 0.157

Asia WGS AF: 0.103 AC: 357 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.3
DANN	Benign	0.50
PhyloP100		-0.24
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: rs3766335; hg19: chr1-78999269;