ENST00000523024.2:n.343+1965T>C

Variant names:

• chr8-10496696-T-G
• ENST00000647727.1:c.596A>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000523024.2(PRSS51):​n.343+1016A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: PRSS51 ENST00000523024.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0350
• Publications: 0 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.054100454).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRSS51	XM_047422509.1	c.596A>C	p.Asn199Thr	missense_variant	Exon 4 of 5		XP_047278465.1
PRSS51	XM_047422510.1	c.335A>C	p.Asn112Thr	missense_variant	Exon 4 of 5		XP_047278466.1
PRSS51	XR_007060817.1	n.673A>C		non_coding_transcript_exon_variant	Exon 4 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRSS51	ENST00000647727.1	c.596A>C	p.Asn199Thr	missense_variant	Exon 4 of 5			ENSP00000497613.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.098
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.3
DANN	Benign	0.71
FATHMM_MKL	Benign	0.010	N
LIST_S2	Benign	0.31	T;T;T;T
MetaRNN	Benign	0.054	T;T;T;T
PhyloP100		0.035
GERP RS		-2.5
Varity_R		0.046
gMVP		0.096
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

hg19: chr8-10354206;