rs2806864

chr1-116927159-C-G

Variant summary

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

The NM_020440.4(PTGFRN):c.50-14556C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 152,082 control chromosomes in the GnomAD database, including 4,466 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 0.17 (4466 hom., cov: 32)
• Consequence: PTGFRN NM_020440.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58

Genes affected

PTGFRN (HGNC:9601): (prostaglandin F2 receptor inhibitor) Predicted to be involved in myoblast fusion involved in skeletal muscle regeneration. Predicted to act upstream of or within lipid droplet organization. Located in cell surface. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.439 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTGFRN	NM_020440.4	c.50-14556C>G		intron_variant		ENST00000393203.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTGFRN	ENST00000393203.3	c.50-14556C>G		intron_variant		1	NM_020440.4	P1

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25159 AN: 151964 Hom.: 4451 Cov.: 32

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.0930

Gnomad ASJ AF: 0.0551

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.0863

Gnomad FIN AF: 0.0979

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0380

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.166 AC: 25218 AN: 152082 Hom.: 4466 Cov.: 32 AF XY: 0.167 AC XY: 12404 AN XY: 74350

Gnomad4 AFR AF: 0.445

Gnomad4 AMR AF: 0.0928

Gnomad4 ASJ AF: 0.0551

Gnomad4 EAS AF: 0.153

Gnomad4 SAS AF: 0.0850

Gnomad4 FIN AF: 0.0979

Gnomad4 NFE AF: 0.0380

Gnomad4 OTH AF: 0.154

Alfa AF: 0.0628 Hom.: 488

Bravo AF: 0.178

Asia WGS AF: 0.144 AC: 499 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.26
Dann	Benign	0.41

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: rs2806864; hg19: chr1-117469781; COSMIC: COSV67797885;