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).

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	ENST00000647727.1		c.596A>C	p.Asn199Thr	missense	Exon 4 of 5	ENSP00000497613.1	A0A3B3ISV0
	PRSS51	ENST00000523024.2	TSL:1	n.343+1016A>C		intron	N/A	ENSP00000518528.1	A0AA34QVK3
	PRSS51	ENST00000647010.1		c.485A>C	p.Asn162Thr	missense	Exon 5 of 6	ENSP00000496218.1	A0A2R8YGP0

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

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
MetaRNN	Benign	0.054	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;