GeneBe

ENST00000523024.2:n.343+2914G>A

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000523024.2(PRSS51):​n.343+1965T>A 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: 33)

Consequence

PRSS51
ENST00000523024.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.282

Publications

0 publications found
Variant links:
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]

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ACMG classification

Classification was made for transcript

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 (BayesDel_noAF=-0.92).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PRSS51XM_047422509.1 linkc.*579T>A 3_prime_UTR_variant Exon 5 of 5 XP_047278465.1
PRSS51XM_047422510.1 linkc.*579T>A 3_prime_UTR_variant Exon 5 of 5 XP_047278466.1
PRSS51XR_007060817.1 linkn.734+888T>A intron_variant Intron 4 of 5

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PRSS51ENST00000523024.2 linkn.343+1965T>A intron_variant Intron 3 of 4 1 ENSP00000518528.1
PRSS51ENST00000647010.1 linkc.*579T>A 3_prime_UTR_variant Exon 6 of 6 ENSP00000496218.1 A0A2R8YGP0
PRSS51ENST00000636217.1 linkc.*638T>A 3_prime_UTR_variant Exon 6 of 6 5 ENSP00000490515.1 A0A1B0GVH4

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
0
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
1.5
DANN
Benign
0.55
PhyloP100
-0.28

Splicing

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

Publications

Other links and lift over

hg19: chr8-10353257; API