rs943371

chr1-116925068-G-C

Variant summary

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

The NM_020440.4(PTGFRN):c.49+14816G>C 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 152,090 control chromosomes in the GnomAD database, including 4,441 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 (4441 hom., cov: 32)
• Consequence: PTGFRN NM_020440.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.800

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=-0.96).
• 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.49+14816G>C		intron_variant		ENST00000393203.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTGFRN	ENST00000393203.3	c.49+14816G>C		intron_variant		1	NM_020440.4	P1

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25115 AN: 151972 Hom.: 4427 Cov.: 32

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.0925

Gnomad ASJ AF: 0.0551

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.0866

Gnomad FIN AF: 0.0979

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0379

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: 25175 AN: 152090 Hom.: 4441 Cov.: 32 AF XY: 0.166 AC XY: 12373 AN XY: 74358

Gnomad4 AFR AF: 0.444

Gnomad4 AMR AF: 0.0923

Gnomad4 ASJ AF: 0.0551

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.0852

Gnomad4 FIN AF: 0.0979

Gnomad4 NFE AF: 0.0379

Gnomad4 OTH AF: 0.154

Alfa AF: 0.109 Hom.: 313

Bravo AF: 0.178

Asia WGS AF: 0.144 AC: 501 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.99
Dann	Benign	0.69

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: rs943371; hg19: chr1-117467690;