rs6686438

chr1-78304263-G-T

Variant summary

Our verdict is Benign. Variant got -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

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=-0.84).
• 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/exons	MANE	UniProt
MGC27382	NR_027310.2	n.706-38263G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTGFR	ENST00000370758.5	c.-148+332G>T		intron_variant		1		P1
MGC27382	ENST00000413519.1	n.683-38263G>T		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.238

Gnomad4 AMR AF: 0.269

Gnomad4 ASJ AF: 0.221

Gnomad4 EAS AF: 0.702

Gnomad4 SAS AF: 0.344

Gnomad4 FIN AF: 0.345

Gnomad4 NFE AF: 0.265

Gnomad4 OTH AF: 0.274

Alfa AF: 0.270 Hom.: 734

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

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: rs6686438; hg19: chr1-78769947;