1-78521617-T-C

Variant names:

• chr1-78521617-T-C
• rs672561
• NM_000959.4:c.799-14789T>C

Variant summary

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

The NM_000959.4(PTGFR):​c.799-14789T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 152,060 control chromosomes in the GnomAD database, including 5,345 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 0.26 (5345 hom., cov: 32)
• Consequence: PTGFR NM_000959.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.84

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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTGFR	NM_000959.4	c.799-14789T>C		intron_variant	Intron 2 of 2	ENST00000370757.8	NP_000950.1
PTGFR	NM_001039585.2	c.870-14789T>C		intron_variant	Intron 3 of 3		NP_001034674.1
PTGFR	XM_047426085.1	c.799-14789T>C		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.799-14789T>C		intron_variant	Intron 2 of 2	1	NM_000959.4	ENSP00000359793.3
PTGFR	ENST00000370758.5	c.799-14789T>C		intron_variant	Intron 3 of 3	1		ENSP00000359794.1
PTGFR	ENST00000370756.3	c.870-14789T>C		intron_variant	Intron 3 of 3	1		ENSP00000359792.3
PTGFR	ENST00000497923.5	n.870-10596T>C		intron_variant	Intron 3 of 4	3		ENSP00000432599.1

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38898 AN: 151942 Hom.: 5344 Cov.: 32

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.264

Gnomad EAS AF: 0.0715

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.256 AC: 38925 AN: 152060 Hom.: 5345 Cov.: 32 AF XY: 0.247 AC XY: 18392 AN XY: 74344

Gnomad4 AFR AF: 0.345

Gnomad4 AMR AF: 0.164

Gnomad4 ASJ AF: 0.264

Gnomad4 EAS AF: 0.0715

Gnomad4 SAS AF: 0.191

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.256

Gnomad4 OTH AF: 0.218

Alfa AF: 0.245 Hom.: 4728

Bravo AF: 0.258

Asia WGS AF: 0.132 AC: 460 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.14
DANN	Benign	0.47

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: rs672561; hg19: chr1-78987302;