chr1-78491756-C-A

Position:

• chr1-78491756-C-A

Variant summary

Our verdict is Benign. Variant got -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

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=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.508 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTGFR	NM_000959.4	c.-73+520C>A		intron_variant		ENST00000370757.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTGFR	ENST00000370757.8	c.-73+520C>A		intron_variant		1	NM_000959.4	P1
PTGFR	ENST00000370756.3	c.-73+520C>A		intron_variant		1
PTGFR	ENST00000370758.5	c.-72-916C>A		intron_variant		1		P1
PTGFR	ENST00000497923.5	c.-73+520C>A		intron_variant, NMD_transcript_variant		3

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

Gnomad4 AFR AF: 0.340

Gnomad4 AMR AF: 0.254

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.524

Gnomad4 SAS AF: 0.217

Gnomad4 FIN AF: 0.146

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.220

Alfa AF: 0.0964 Hom.: 190

Bravo AF: 0.231

Asia WGS AF: 0.353 AC: 1227 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	0.37
DANN	Benign	0.76

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: rs3766355; hg19: chr1-78957441;