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 XM_047422509.1(PRSS51):​c.*1528G>T variant causes a 3 prime UTR 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 XM_047422509.1 3_prime_UTR
• 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000523024.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRSS51	ENST00000523024.2	TSL:1	n.343+2914G>T		intron	N/A	ENSP00000518528.1	A0AA34QVK3
	PRSS51	ENST00000521149.2	TSL:5	n.203+3930G>T		intron	N/A
	PRSS51	ENST00000647010.1		c.*1528G>T		downstream_gene	N/A	ENSP00000496218.1	A0A2R8YGP0

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 v4.9

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;