rs17882368

chr16-31089001-G-Achr16-31089001-G-Cchr16-31089001-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000486499.1(PRSS53):n.628C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00214 in 1,387,514 control chromosomes in the GnomAD database, including 28 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 0.0076 (16 hom., cov: 32)
  • Exomes 𝑓: 0.0015 (12 hom.)
• Consequence: PRSS53 ENST00000486499.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.14

Genes affected

PRSS53 (HGNC:34407): (serine protease 53) Predicted to enable serine-type endopeptidase activity. Predicted to be involved in proteolysis. Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00764 (1164/152376) while in subpopulation AFR AF= 0.0242 (1005/41584). AF 95% confidence interval is 0.0229. There are 16 homozygotes in gnomad4. There are 552 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 16 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRSS53	ENST00000486499.1	n.628C>T		non_coding_transcript_exon_variant	1/2	2

Frequencies

GnomAD3 genomes AF: 0.00764 AC: 1164 AN: 152258 Hom.: 16 Cov.: 32

Gnomad AFR AF: 0.0243

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00314

Gnomad ASJ AF: 0.000576

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000188

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00122

Gnomad OTH AF: 0.00669

GnomAD4 exome AF: 0.00146 AC: 1807 AN: 1235138 Hom.: 12 Cov.: 20 AF XY: 0.00140 AC XY: 841 AN XY: 599814

Gnomad4 AFR exome AF: 0.0274

Gnomad4 AMR exome AF: 0.00200

Gnomad4 ASJ exome AF: 0.000107

Gnomad4 EAS exome AF: 0.000409

Gnomad4 SAS exome AF: 0.000127

Gnomad4 FIN exome AF: 0.000641

Gnomad4 NFE exome AF: 0.000840

Gnomad4 OTH exome AF: 0.00249

GnomAD4 genome AF: 0.00764 AC: 1164 AN: 152376 Hom.: 16 Cov.: 32 AF XY: 0.00741 AC XY: 552 AN XY: 74518

Gnomad4 AFR AF: 0.0242

Gnomad4 AMR AF: 0.00314

Gnomad4 ASJ AF: 0.000576

Gnomad4 EAS AF: 0.00115

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000188

Gnomad4 NFE AF: 0.00122

Gnomad4 OTH AF: 0.00756

Alfa AF: 0.00317 Hom.: 1

Bravo AF: 0.00868

Asia WGS AF: 0.00346 AC: 12 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.010
Dann	Benign	0.29

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: rs17882368; hg19: chr16-31100322;