rs10086950

Positions:

• chr8-10497868-C-A

Variant summary

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

The ENST00000647727.1(PRSS51):​c.358G>T​(p.Asp120Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 398,772 control chromosomes in the GnomAD database, including 17,773 homozygotes. In-silico tool predicts a benign outcome for this variant. 5/7 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.28 (6141 hom., cov: 32)
  • Exomes 𝑓: 0.30 (11632 hom.)
• Consequence: PRSS51 ENST00000647727.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.06

Genes affected

PRSS51 (HGNC:37321): (serine protease 51) 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]

PRSS51 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.0023303628).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRSS51	XM_047422509.1	c.358G>T	p.Asp120Tyr	missense_variant	3/5		XP_047278465.1
PRSS51	XM_047422510.1	c.97G>T	p.Asp33Tyr	missense_variant	3/5		XP_047278466.1
PRSS51	XR_007060817.1	n.435G>T		non_coding_transcript_exon_variant	3/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRSS51	ENST00000647727.1	c.358G>T	p.Asp120Tyr	missense_variant	3/5			ENSP00000497613.1

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42292 AN: 151918 Hom.: 6129 Cov.: 32

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.259

GnomAD4 exome AF: 0.303 AC: 74864 AN: 246736 Hom.: 11632 Cov.: 0 AF XY: 0.303 AC XY: 37876 AN XY: 125060

Gnomad4 AFR exome AF: 0.187

Gnomad4 AMR exome AF: 0.317

Gnomad4 ASJ exome AF: 0.199

Gnomad4 EAS exome AF: 0.290

Gnomad4 SAS exome AF: 0.224

Gnomad4 FIN exome AF: 0.311

Gnomad4 NFE exome AF: 0.320

Gnomad4 OTH exome AF: 0.278

GnomAD4 genome AF: 0.278 AC: 42334 AN: 152036 Hom.: 6141 Cov.: 32 AF XY: 0.279 AC XY: 20759 AN XY: 74310

Gnomad4 AFR AF: 0.186

Gnomad4 AMR AF: 0.334

Gnomad4 ASJ AF: 0.199

Gnomad4 EAS AF: 0.326

Gnomad4 SAS AF: 0.220

Gnomad4 FIN AF: 0.306

Gnomad4 NFE AF: 0.324

Gnomad4 OTH AF: 0.261

Alfa AF: 0.308 Hom.: 15279

Bravo AF: 0.276

TwinsUK AF: 0.315 AC: 1168

ALSPAC AF: 0.315 AC: 1215

Asia WGS AF: 0.244 AC: 845 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	20
DANN	Benign	0.68
FATHMM_MKL	Benign	0.018	N
LIST_S2	Benign	0.51	T
MetaRNN	Benign	0.0023	T
GERP RS		2.1
gMVP		0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10086950; hg19: chr8-10355378;