rs4281086

Variant names:

• chr8-10494798-C-A
• rs4281086
• ENST00000523024.2:n.343+2914G>T

Your query was ambiguous. Multiple possible variants found:

• chr8-10494798-C-A
• chr8-10494798-C-G
• chr8-10494798-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000523024.2(PRSS51):​n.343+2914G>T variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.885
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PRSS51	XM_047422509.1	c.*1528G>T		3_prime_UTR_variant	Exon 5 of 5		XP_047278465.1
PRSS51	XM_047422510.1	c.*1528G>T		3_prime_UTR_variant	Exon 5 of 5		XP_047278466.1
PRSS51	XR_007060817.1	n.734+1837G>T		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRSS51	ENST00000523024.2	n.343+2914G>T		intron_variant	Intron 3 of 4	1		ENSP00000518528.1
PRSS51	ENST00000521149.2	n.203+3930G>T		intron_variant	Intron 2 of 2	5
PRSS51	ENST00000647010.1	c.*1528G>T		downstream_gene_variant				ENSP00000496218.1

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

African (AFR) AF: 0.675 AC: 27991 AN: 41470

American (AMR) AF: 0.684 AC: 10447 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.505 AC: 1749 AN: 3464

East Asian (EAS) AF: 0.671 AC: 3473 AN: 5172

South Asian (SAS) AF: 0.701 AC: 3384 AN: 4824

European-Finnish (FIN) AF: 0.644 AC: 6802 AN: 10562

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.654 AC: 44446 AN: 67988

Other (OTH) AF: 0.628 AC: 1326 AN: 2110

Alfa AF: 0.658 Hom.: 21923

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
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs4281086; hg19: chr8-10352308;