rs12359728

chr10-108296563-A-G

Variant summary

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

The 10-108296563-A-G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0371 in 152,614 control chromosomes in the GnomAD database, including 265 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 0.037 (265 hom., cov: 32)
  • Exomes 𝑓: 0.011 (0 hom.)
• Consequence: PTGES3P5 ENST00000455109.2 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.73

Genes affected

PTGES3P5 (HGNC:43826): (prostaglandin E synthase 3 pseudogene 5)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.161 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTGES3P5	ENST00000455109.2			downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.0371 AC: 5639 AN: 152130 Hom.: 258 Cov.: 32

Gnomad AFR AF: 0.00763

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0900

Gnomad ASJ AF: 0.0242

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.00678

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0323

Gnomad OTH AF: 0.0446

GnomAD4 exome AF: 0.0109 AC: 4 AN: 366 Hom.: 0 Cov.: 0 AF XY: 0.0169 AC XY: 3 AN XY: 178

Gnomad4 FIN exome AF: 0.00824

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.0371 AC: 5656 AN: 152248 Hom.: 265 Cov.: 32 AF XY: 0.0395 AC XY: 2937 AN XY: 74440

Gnomad4 AFR AF: 0.00760

Gnomad4 AMR AF: 0.0910

Gnomad4 ASJ AF: 0.0242

Gnomad4 EAS AF: 0.171

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.00678

Gnomad4 NFE AF: 0.0323

Gnomad4 OTH AF: 0.0441

Alfa AF: 0.0310 Hom.: 18

Bravo AF: 0.0425

Asia WGS AF: 0.137 AC: 473 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	6.8
Dann	Benign	0.70

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs12359728; hg19: chr10-110056321;