chr9-111585121-T-C

Variant names:

• chr9-111585121-T-C
• rs10120479
• NM_001146108.2:c.377+877A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001146108.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTGR1	NM_001146108.2	MANE Select	c.377+877A>G		intron	N/A	NP_001139580.1
	PTGR1	NM_012212.3		c.377+877A>G		intron	N/A	NP_036344.2
	PTGR1	NM_001146109.2		c.377+877A>G		intron	N/A	NP_001139581.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTGR1	ENST00000407693.7	TSL:1 MANE Select	c.377+877A>G		intron	N/A	ENSP00000385763.2
	PTGR1	ENST00000309195.9	TSL:1	c.377+877A>G		intron	N/A	ENSP00000311572.5
	PTGR1	ENST00000538962.7	TSL:2	c.377+877A>G		intron	N/A	ENSP00000440281.1

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

African (AFR) AF: 0.166 AC: 6901 AN: 41450

American (AMR) AF: 0.0539 AC: 824 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0608 AC: 211 AN: 3470

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5180

South Asian (SAS) AF: 0.0356 AC: 171 AN: 4806

European-Finnish (FIN) AF: 0.0315 AC: 333 AN: 10566

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0566 AC: 3849 AN: 67978

Other (OTH) AF: 0.0750 AC: 158 AN: 2106

Alfa AF: 0.0726 Hom.: 771

Bravo AF: 0.0853

Asia WGS AF: 0.0300 AC: 104 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.2
DANN	Benign	0.84
PhyloP100		0.24
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: rs10120479; hg19: chr9-114347401;