rs6686438

Variant names:

• chr1-78304263-G-T
• rs6686438
• ENST00000370758.5:c.-148+332G>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+332G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.281 in 151,980 control chromosomes in the GnomAD database, including 6,660 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 0.28 (6660 hom., cov: 32)
• Consequence: PTGFR ENST00000370758.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.57
• Publications: 7 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.683 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MGC27382	NR_027310.2	n.706-38263G>T		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTGFR	ENST00000370758.5	c.-148+332G>T		intron_variant	Intron 1 of 3	1		ENSP00000359794.1
MGC27382	ENST00000413519.1	n.683-38263G>T		intron_variant	Intron 3 of 5	2

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42614 AN: 151862 Hom.: 6657 Cov.: 32

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.702

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.281 AC: 42647 AN: 151980 Hom.: 6660 Cov.: 32 AF XY: 0.288 AC XY: 21421 AN XY: 74282

African (AFR) AF: 0.238 AC: 9864 AN: 41456

American (AMR) AF: 0.269 AC: 4107 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.221 AC: 764 AN: 3464

East Asian (EAS) AF: 0.702 AC: 3628 AN: 5168

South Asian (SAS) AF: 0.344 AC: 1661 AN: 4822

European-Finnish (FIN) AF: 0.345 AC: 3649 AN: 10564

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.265 AC: 17989 AN: 67924

Other (OTH) AF: 0.274 AC: 577 AN: 2106

Alfa AF: 0.269 Hom.: 756

Bravo AF: 0.273

Asia WGS AF: 0.471 AC: 1632 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.2
DANN	Benign	0.27
PhyloP100		1.6
PromoterAI		0.0070	Neutral
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: rs6686438; hg19: chr1-78769947;