rs4620527

Positions:

• chr1-116987999-A-G

Variant summary

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

The NM_020440.4(PTGFRN):​c.*1032A>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 0.2 in 152,198 control chromosomes in the GnomAD database, including 3,899 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 0.20 (3898 hom., cov: 32)
  • Exomes 𝑓: 0.25 (1 hom.)
• Consequence: PTGFRN NM_020440.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31

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 (AMR) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PTGFRN	NM_020440.4	c.*1032A>G		3_prime_UTR_variant	9/9	ENST00000393203.3	NP_065173.2
PTGFRN	XM_017001874.2	c.*1032A>G		3_prime_UTR_variant	9/9		XP_016857363.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PTGFRN	ENST00000393203.3	c.*1032A>G		3_prime_UTR_variant	9/9	1	NM_020440.4	ENSP00000376899	P1
PTGFRN	ENST00000497385.1	n.45+915A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.200 AC: 30394 AN: 152056 Hom.: 3882 Cov.: 32

Gnomad AFR AF: 0.0484

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.217

GnomAD4 exome AF: 0.250 AC: 6 AN: 24 Hom.: 1 Cov.: 0 AF XY: 0.227 AC XY: 5 AN XY: 22

Gnomad4 ASJ exome AF: 0.00

Gnomad4 NFE exome AF: 0.278

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.200 AC: 30419 AN: 152174 Hom.: 3898 Cov.: 32 AF XY: 0.207 AC XY: 15433 AN XY: 74376

Gnomad4 AFR AF: 0.0482

Gnomad4 AMR AF: 0.360

Gnomad4 ASJ AF: 0.229

Gnomad4 EAS AF: 0.201

Gnomad4 SAS AF: 0.296

Gnomad4 FIN AF: 0.283

Gnomad4 NFE AF: 0.235

Gnomad4 OTH AF: 0.222

Alfa AF: 0.217 Hom.: 512

Bravo AF: 0.200

Asia WGS AF: 0.282 AC: 977 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	0.70
DANN	Benign	0.47

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: rs4620527; hg19: chr1-117530621;