1-78360228-C-T

Variant names:

• chr1-78360228-C-T
• rs7533564
• ENST00000370758.5:c.-147-38723C>T

Variant summary

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

The ENST00000370758.5(PTGFR):​c.-147-38723C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.924 in 152,288 control chromosomes in the GnomAD database, including 65,582 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 0.92 (65582 hom., cov: 33)
• Consequence: PTGFR ENST00000370758.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0620
• 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]

MGC27382 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MGC27382	NR_027310.2	n.821-8309C>T		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTGFR	ENST00000370758.5	c.-147-38723C>T		intron_variant	Intron 1 of 3	1		ENSP00000359794.1
MGC27382	ENST00000413519.1	n.798-8309C>T		intron_variant	Intron 4 of 5	2

Frequencies

GnomAD3 genomes AF: 0.924 AC: 140674 AN: 152170 Hom.: 65536 Cov.: 33

Gnomad AFR AF: 0.794

Gnomad AMI AF: 0.891

Gnomad AMR AF: 0.968

Gnomad ASJ AF: 0.976

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.883

Gnomad FIN AF: 0.990

Gnomad MID AF: 0.956

Gnomad NFE AF: 0.979

Gnomad OTH AF: 0.942

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

GnomAD4 genome AF: 0.924 AC: 140776 AN: 152288 Hom.: 65582 Cov.: 33 AF XY: 0.925 AC XY: 68868 AN XY: 74464

African (AFR) AF: 0.794 AC: 32965 AN: 41524

American (AMR) AF: 0.968 AC: 14816 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.976 AC: 3387 AN: 3472

East Asian (EAS) AF: 0.998 AC: 5168 AN: 5176

South Asian (SAS) AF: 0.883 AC: 4263 AN: 4828

European-Finnish (FIN) AF: 0.990 AC: 10511 AN: 10620

Middle Eastern (MID) AF: 0.952 AC: 280 AN: 294

European-Non Finnish (NFE) AF: 0.979 AC: 66582 AN: 68044

Other (OTH) AF: 0.942 AC: 1991 AN: 2114

Alfa AF: 0.957 Hom.: 98853

Bravo AF: 0.919

Asia WGS AF: 0.938 AC: 3262 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	0.93
DANN	Benign	0.41
PhyloP100		-0.062
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: rs7533564; hg19: chr1-78825912;