1-116980379-A-G

Variant names:

• chr1-116980379-A-G
• rs7552382
• NM_020440.4:c.2168-4301A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020440.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTGFRN	NM_020440.4	MANE Select	c.2168-4301A>G		intron	N/A	NP_065173.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTGFRN	ENST00000393203.3	TSL:1 MANE Select	c.2168-4301A>G		intron	N/A	ENSP00000376899.2	Q9P2B2
	PTGFRN	ENST00000881332.1		c.2060-4301A>G		intron	N/A	ENSP00000551391.1

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

African (AFR) AF: 0.451 AC: 18696 AN: 41498

American (AMR) AF: 0.262 AC: 4009 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 862 AN: 3472

East Asian (EAS) AF: 0.464 AC: 2400 AN: 5176

South Asian (SAS) AF: 0.342 AC: 1648 AN: 4822

European-Finnish (FIN) AF: 0.263 AC: 2782 AN: 10586

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.299 AC: 20356 AN: 67986

Other (OTH) AF: 0.324 AC: 684 AN: 2114

Alfa AF: 0.327 Hom.: 1353

Bravo AF: 0.344

Asia WGS AF: 0.346 AC: 1202 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.2
DANN	Benign	0.21
PhyloP100		0.16
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7552382; hg19: chr1-117523001;