1-116926891-A-G

Variant names:

• chr1-116926891-A-G
• rs2806863
• NM_020440.4:c.50-14824A>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.50-14824A>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 152,140 control chromosomes in the GnomAD database, including 4,452 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 (4452 hom., cov: 32)
• Consequence: PTGFRN NM_020440.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.122
• Publications: 2 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=-0.96).
• 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 rank	MANE	Protein	UniProt
PTGFRN	NM_020440.4	c.50-14824A>G		intron_variant	Intron 1 of 8	ENST00000393203.3	NP_065173.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTGFRN	ENST00000393203.3	c.50-14824A>G		intron_variant	Intron 1 of 8	1	NM_020440.4	ENSP00000376899.2

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25151 AN: 152022 Hom.: 4438 Cov.: 32

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.0176

Gnomad AMR AF: 0.0926

Gnomad ASJ AF: 0.0551

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.0860

Gnomad FIN AF: 0.0978

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: 25211 AN: 152140 Hom.: 4452 Cov.: 32 AF XY: 0.167 AC XY: 12388 AN XY: 74378

African (AFR) AF: 0.444 AC: 18419 AN: 41454

American (AMR) AF: 0.0924 AC: 1414 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0551 AC: 191 AN: 3466

East Asian (EAS) AF: 0.151 AC: 781 AN: 5176

South Asian (SAS) AF: 0.0846 AC: 408 AN: 4822

European-Finnish (FIN) AF: 0.0978 AC: 1036 AN: 10596

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.0380 AC: 2581 AN: 68000

Other (OTH) AF: 0.154 AC: 326 AN: 2116

Alfa AF: 0.0574 Hom.: 175

Bravo AF: 0.178

Asia WGS AF: 0.144 AC: 501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.8
DANN	Benign	0.41
PhyloP100		0.12
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: rs2806863; hg19: chr1-117469513;