rs6672484

chr1-78327963-C-T

Variant summary

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

The ENST00000370758.5(PTGFR):c.-148+24032C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.23 in 151,682 control chromosomes in the GnomAD database, including 4,255 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 0.23 (4255 hom., cov: 32)
• Consequence: PTGFR ENST00000370758.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.27

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MGC27382	NR_027310.2	n.706-14563C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTGFR	ENST00000370758.5	c.-148+24032C>T		intron_variant		1		P1
MGC27382	ENST00000413519.1	n.683-14563C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.230 AC: 34872 AN: 151564 Hom.: 4259 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.0513

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.230 AC: 34866 AN: 151682 Hom.: 4255 Cov.: 32 AF XY: 0.226 AC XY: 16755 AN XY: 74070

Gnomad4 AFR AF: 0.186

Gnomad4 AMR AF: 0.175

Gnomad4 ASJ AF: 0.334

Gnomad4 EAS AF: 0.0509

Gnomad4 SAS AF: 0.238

Gnomad4 FIN AF: 0.255

Gnomad4 NFE AF: 0.272

Gnomad4 OTH AF: 0.240

Alfa AF: 0.256 Hom.: 622

Bravo AF: 0.221

Asia WGS AF: 0.143 AC: 505 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.87
Dann	Benign	0.84

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: rs6672484; hg19: chr1-78793647; COSMIC: COSV66120942;