rs4281086

chr8-10494798-C-Achr8-10494798-C-Gchr8-10494798-C-T

Variant summary

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

The ENST00000523024.2(PRSS51):c.343+2914G>T variant causes a intron, NMD transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.658 in 152,062 control chromosomes in the GnomAD database, including 33,180 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 0.66 (33180 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: PRSS51 ENST00000523024.2 intron, NMD_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.885

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.682 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRSS51	XR_007060820.1	n.635+2914G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRSS51	ENST00000523024.2	c.343+2914G>T		intron_variant, NMD_transcript_variant		1
PRSS51	ENST00000521149.2	n.203+3930G>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.658 AC: 99991 AN: 151944 Hom.: 33130 Cov.: 32

Gnomad AFR AF: 0.675

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.684

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.672

Gnomad SAS AF: 0.701

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.654

Gnomad OTH AF: 0.626

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

GnomAD4 genome AF: 0.658 AC: 100103 AN: 152062 Hom.: 33180 Cov.: 32 AF XY: 0.660 AC XY: 49052 AN XY: 74316

Gnomad4 AFR AF: 0.675

Gnomad4 AMR AF: 0.684

Gnomad4 ASJ AF: 0.505

Gnomad4 EAS AF: 0.671

Gnomad4 SAS AF: 0.701

Gnomad4 FIN AF: 0.644

Gnomad4 NFE AF: 0.654

Gnomad4 OTH AF: 0.628

Alfa AF: 0.656 Hom.: 11168

Bravo AF: 0.656

Asia WGS AF: 0.676 AC: 2351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.44
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4281086; hg19: chr8-10352308;