chr1-116980379-A-G

Position:

• chr1-116980379-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.2168-4301A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 152,148 control chromosomes in the GnomAD database, including 9,240 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 0.34 (9240 hom., cov: 32)
• Consequence: PTGFRN NM_020440.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164

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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PTGFRN	NM_020440.4	c.2168-4301A>G		intron_variant		ENST00000393203.3	NP_065173.2
PTGFRN	XM_017001874.2	c.2186-4301A>G		intron_variant			XP_016857363.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PTGFRN	ENST00000393203.3	c.2168-4301A>G		intron_variant		1	NM_020440.4	ENSP00000376899.2

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51897 AN: 152030 Hom.: 9244 Cov.: 32

Gnomad AFR AF: 0.451

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.464

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.341 AC: 51941 AN: 152148 Hom.: 9240 Cov.: 32 AF XY: 0.340 AC XY: 25314 AN XY: 74394

Gnomad4 AFR AF: 0.451

Gnomad4 AMR AF: 0.262

Gnomad4 ASJ AF: 0.248

Gnomad4 EAS AF: 0.464

Gnomad4 SAS AF: 0.342

Gnomad4 FIN AF: 0.263

Gnomad4 NFE AF: 0.299

Gnomad4 OTH AF: 0.324

Alfa AF: 0.323 Hom.: 1275

Bravo AF: 0.344

Asia WGS AF: 0.346 AC: 1202 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.2
DANN	Benign	0.21

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: rs7552382; hg19: chr1-117523001;