rs6672484

Variant names:

• chr1-78327963-C-T
• rs6672484
• ENST00000370758.5:c.-148+24032C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000370758.5. 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
	MGC27382	NR_027310.2		n.706-14563C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTGFR	ENST00000370758.5	TSL:1	c.-148+24032C>T		intron	N/A	ENSP00000359794.1	P43088-1
	MGC27382	ENST00000413519.1	TSL:2	n.683-14563C>T		intron	N/A

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

African (AFR) AF: 0.186 AC: 7707 AN: 41374

American (AMR) AF: 0.175 AC: 2663 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.334 AC: 1159 AN: 3468

East Asian (EAS) AF: 0.0509 AC: 261 AN: 5132

South Asian (SAS) AF: 0.238 AC: 1143 AN: 4802

European-Finnish (FIN) AF: 0.255 AC: 2678 AN: 10502

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.272 AC: 18485 AN: 67870

Other (OTH) AF: 0.240 AC: 506 AN: 2104

Alfa AF: 0.253 Hom.: 632

Bravo AF: 0.221

Asia WGS AF: 0.143 AC: 505 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.87
DANN	Benign	0.84
PhyloP100		-2.3
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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6672484;

hg19: chr1-78793647;

COSMIC: COSV66120942;