rs10306148

Positions:

• chr9-122381105-C-G

Variant summary

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

The NM_000962.4(PTGS1):​c.497-266C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 152,166 control chromosomes in the GnomAD database, including 8,659 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 0.27 (8659 hom., cov: 33)
• Consequence: PTGS1 NM_000962.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.315

Genes affected

PTGS1 (HGNC:9604): (prostaglandin-endoperoxide synthase 1) This is one of two genes encoding similar enzymes that catalyze the conversion of arachidonate to prostaglandin. The encoded protein regulates angiogenesis in endothelial cells, and is inhibited by nonsteroidal anti-inflammatory drugs such as aspirin. Based on its ability to function as both a cyclooxygenase and as a peroxidase, the encoded protein has been identified as a moonlighting protein. The protein may promote cell proliferation during tumor progression. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2021]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.583 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTGS1	NM_000962.4	c.497-266C>G		intron_variant		ENST00000362012.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTGS1	ENST00000362012.7	c.497-266C>G		intron_variant		1	NM_000962.4	P1

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40413 AN: 152048 Hom.: 8621 Cov.: 33

Gnomad AFR AF: 0.589

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.0444

Gnomad SAS AF: 0.0906

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.266 AC: 40506 AN: 152166 Hom.: 8659 Cov.: 33 AF XY: 0.262 AC XY: 19473 AN XY: 74396

Gnomad4 AFR AF: 0.590

Gnomad4 AMR AF: 0.240

Gnomad4 ASJ AF: 0.122

Gnomad4 EAS AF: 0.0445

Gnomad4 SAS AF: 0.0902

Gnomad4 FIN AF: 0.130

Gnomad4 NFE AF: 0.136

Gnomad4 OTH AF: 0.241

Alfa AF: 0.226 Hom.: 793

Bravo AF: 0.288

Asia WGS AF: 0.118 AC: 413 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.082
DANN	Benign	0.42

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: rs10306148; hg19: chr9-125143384;