9-111585121-T-C

Position:

• chr9-111585121-T-C

Variant summary

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

The NM_001146108.2(PTGR1):​c.377+877A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0822 in 152,040 control chromosomes in the GnomAD database, including 771 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 0.082 (771 hom., cov: 32)
• Consequence: PTGR1 NM_001146108.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.244

Genes affected

PTGR1 (HGNC:18429): (prostaglandin reductase 1) This gene encodes an enzyme that is involved in the inactivation of the chemotactic factor, leukotriene B4. The encoded protein specifically catalyzes the NADP+ dependent conversion of leukotriene B4 to 12-oxo-leukotriene B4. A pseudogene of this gene is found on chromosome 1. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.163 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTGR1	NM_001146108.2	c.377+877A>G		intron_variant		ENST00000407693.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTGR1	ENST00000407693.7	c.377+877A>G		intron_variant		1	NM_001146108.2	P1

Frequencies

GnomAD3 genomes AF: 0.0822 AC: 12483 AN: 151932 Hom.: 772 Cov.: 32

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.0297

Gnomad AMR AF: 0.0540

Gnomad ASJ AF: 0.0608

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0359

Gnomad FIN AF: 0.0315

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0566

Gnomad OTH AF: 0.0758

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

GnomAD4 genome AF: 0.0822 AC: 12495 AN: 152040 Hom.: 771 Cov.: 32 AF XY: 0.0794 AC XY: 5902 AN XY: 74326

Gnomad4 AFR AF: 0.166

Gnomad4 AMR AF: 0.0539

Gnomad4 ASJ AF: 0.0608

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0356

Gnomad4 FIN AF: 0.0315

Gnomad4 NFE AF: 0.0566

Gnomad4 OTH AF: 0.0750

Alfa AF: 0.0603 Hom.: 304

Bravo AF: 0.0853

Asia WGS AF: 0.0300 AC: 104 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.2
DANN	Benign	0.84

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: rs10120479; hg19: chr9-114347401;