NM_000959.4:c.*217A>G

Variant names:

• chr1-78536904-A-G
• rs12731181
• NM_000959.4:c.*217A>G

Variant summary

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

The NM_000959.4(PTGFR):​c.*217A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 533,852 control chromosomes in the GnomAD database, including 7,084 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 0.15 (1869 hom., cov: 32)
  • Exomes 𝑓: 0.16 (5215 hom.)
• Consequence: PTGFR NM_000959.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.405

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTGFR	NM_000959.4	c.*217A>G		3_prime_UTR_variant	Exon 3 of 3	ENST00000370757.8	NP_000950.1
PTGFR	NM_001039585.2	c.*474A>G		3_prime_UTR_variant	Exon 4 of 4		NP_001034674.1
PTGFR	XM_047426085.1	c.*217A>G		3_prime_UTR_variant	Exon 3 of 3		XP_047282041.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTGFR	ENST00000370757.8	c.*217A>G		3_prime_UTR_variant	Exon 3 of 3	1	NM_000959.4	ENSP00000359793.3

Frequencies

GnomAD3 genomes AF: 0.152 AC: 23133 AN: 152006 Hom.: 1864 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.0164

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.132

GnomAD4 exome AF: 0.157 AC: 59779 AN: 381728 Hom.: 5215 Cov.: 5 AF XY: 0.156 AC XY: 31066 AN XY: 198976

Gnomad4 AFR exome AF: 0.146

Gnomad4 AMR exome AF: 0.0889

Gnomad4 ASJ exome AF: 0.121

Gnomad4 EAS exome AF: 0.0119

Gnomad4 SAS exome AF: 0.138

Gnomad4 FIN exome AF: 0.137

Gnomad4 NFE exome AF: 0.182

Gnomad4 OTH exome AF: 0.148

GnomAD4 genome AF: 0.152 AC: 23164 AN: 152124 Hom.: 1869 Cov.: 32 AF XY: 0.148 AC XY: 10996 AN XY: 74364

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.101

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.0164

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.184

Gnomad4 OTH AF: 0.131

Alfa AF: 0.175 Hom.: 601

Bravo AF: 0.148

Asia WGS AF: 0.0790 AC: 274 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.9
DANN	Benign	0.58

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: rs12731181; hg19: chr1-79002589;