rs3766355

Variant names:

• chr1-78491756-C-A
• rs3766355
• NM_000959.4:c.-73+520C>A

Your query was ambiguous. Multiple possible variants found:

• chr1-78491756-C-A
• chr1-78491756-C-G
• chr1-78491756-C-T

Variant summary

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

The NM_000959.4(PTGFR):​c.-73+520C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.214 in 152,110 control chromosomes in the GnomAD database, including 4,399 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 0.21 (4399 hom., cov: 33)
• Consequence: PTGFR NM_000959.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54
• Publications: 16 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=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.508 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000959.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTGFR	NM_000959.4	MANE Select	c.-73+520C>A		intron	N/A	NP_000950.1	P43088-1
	PTGFR	NM_001039585.2		c.-73+520C>A		intron	N/A	NP_001034674.1	P43088-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTGFR	ENST00000370757.8	TSL:1 MANE Select	c.-73+520C>A		intron	N/A	ENSP00000359793.3	P43088-1
	PTGFR	ENST00000370758.5	TSL:1	c.-72-916C>A		intron	N/A	ENSP00000359794.1	P43088-1
	PTGFR	ENST00000370756.3	TSL:1	c.-73+520C>A		intron	N/A	ENSP00000359792.3	P43088-2

Frequencies

GnomAD3 genomes AF: 0.214 AC: 32549 AN: 151992 Hom.: 4388 Cov.: 33

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.214 AC: 32608 AN: 152110 Hom.: 4399 Cov.: 33 AF XY: 0.219 AC XY: 16289 AN XY: 74386

African (AFR) AF: 0.340 AC: 14076 AN: 41460

American (AMR) AF: 0.254 AC: 3883 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 460 AN: 3472

East Asian (EAS) AF: 0.524 AC: 2705 AN: 5160

South Asian (SAS) AF: 0.217 AC: 1047 AN: 4822

European-Finnish (FIN) AF: 0.146 AC: 1541 AN: 10588

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.120 AC: 8164 AN: 68002

Other (OTH) AF: 0.220 AC: 465 AN: 2110

Alfa AF: 0.157 Hom.: 4090

Bravo AF: 0.231

Asia WGS AF: 0.353 AC: 1227 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	0.37
DANN	Benign	0.76
PhyloP100		-1.5
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: rs3766355; hg19: chr1-78957441;