NM_025072.7:c.280-136G>T

Variant names:

• chr9-128125577-C-A
• rs884115
• NM_025072.7:c.280-136G>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_025072.7(PTGES2):​c.280-136G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000153 in 654,250 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000015 (0 hom.)
• Consequence: PTGES2 NM_025072.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.82
• Publications: 0 publications found

Genes affected

PTGES2 (HGNC:17822): (prostaglandin E synthase 2) The protein encoded by this gene is a membrane-associated prostaglandin E synthase, which catalyzes the conversion of prostaglandin H2 to prostaglandin E2. This protein also has been shown to activate the transcription regulated by a gamma-interferon-activated transcription element (GATE). Multiple transcript variants have been found for this gene. [provided by RefSeq, Jun 2009]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_025072.7. 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
	PTGES2	NM_025072.7	MANE Select	c.280-136G>T		intron	N/A	NP_079348.1
	PTGES2	NM_001256335.2		c.-198-136G>T		intron	N/A	NP_001243264.1
	PTGES2	NM_198938.3		c.-387-136G>T		intron	N/A	NP_945176.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTGES2	ENST00000338961.11	TSL:1 MANE Select	c.280-136G>T		intron	N/A	ENSP00000345341.6
	PTGES2	ENST00000930205.1		c.280-136G>T		intron	N/A	ENSP00000600264.1
	PTGES2	ENST00000930204.1		c.280-136G>T		intron	N/A	ENSP00000600263.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000153 AC: 1 AN: 654250 Hom.: 0 AF XY: 0.00000295 AC XY: 1 AN XY: 338706

African (AFR) AF: 0.00 AC: 0 AN: 16766

American (AMR) AF: 0.00 AC: 0 AN: 26052

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 16202

East Asian (EAS) AF: 0.00 AC: 0 AN: 32330

South Asian (SAS) AF: 0.00 AC: 0 AN: 53640

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 32364

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2398

European-Non Finnish (NFE) AF: 0.00000227 AC: 1 AN: 441468

Other (OTH) AF: 0.00 AC: 0 AN: 33030

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.14
DANN	Benign	0.26
PhyloP100		-3.8

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs884115; hg19: chr9-130887856;