7-142752026-C-G

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBP7

The NM_002769.5(PRSS1):ā€‹c.453C>Gā€‹(p.Gly151Gly) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: š‘“ 0.00046 ( 0 hom., cov: 30)
Exomes š‘“: 0.000038 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

PRSS1
NM_002769.5 splice_region, synonymous

Scores

2
Splicing: ADA: 0.0006134
2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.21
Variant links:
Genes affected
PRSS1 (HGNC:9475): (serine protease 1) This gene encodes a trypsinogen, which is a member of the trypsin family of serine proteases. This enzyme is secreted by the pancreas and cleaved to its active form in the small intestine. It is active on peptide linkages involving the carboxyl group of lysine or arginine. Mutations in this gene are associated with hereditary pancreatitis. This gene and several other trypsinogen genes are localized to the T cell receptor beta locus on chromosome 7. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.64).
BP7
Synonymous conserved (PhyloP=-2.21 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PRSS1NM_002769.5 linkuse as main transcriptc.453C>G p.Gly151Gly splice_region_variant, synonymous_variant 3/5 ENST00000311737.12 NP_002760.1 P07477

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PRSS1ENST00000311737.12 linkuse as main transcriptc.453C>G p.Gly151Gly splice_region_variant, synonymous_variant 3/51 NM_002769.5 ENSP00000308720.7 P07477

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
58
AN:
125976
Hom.:
0
Cov.:
30
FAILED QC
Gnomad AFR
AF:
0.000494
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000319
Gnomad ASJ
AF:
0.000339
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.000118
Gnomad MID
AF:
0.00352
Gnomad NFE
AF:
0.000571
Gnomad OTH
AF:
0.00118
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.0000382
AC:
50
AN:
1309612
Hom.:
0
Cov.:
60
AF XY:
0.0000397
AC XY:
26
AN XY:
655004
show subpopulations
Gnomad4 AFR exome
AF:
0.000107
Gnomad4 AMR exome
AF:
0.0000514
Gnomad4 ASJ exome
AF:
0.0000857
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000121
Gnomad4 FIN exome
AF:
0.000605
Gnomad4 NFE exome
AF:
0.00000607
Gnomad4 OTH exome
AF:
0.0000180
GnomAD4 genome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.000460
AC:
58
AN:
126030
Hom.:
0
Cov.:
30
AF XY:
0.000554
AC XY:
34
AN XY:
61348
show subpopulations
Gnomad4 AFR
AF:
0.000493
Gnomad4 AMR
AF:
0.000319
Gnomad4 ASJ
AF:
0.000339
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.000118
Gnomad4 NFE
AF:
0.000571
Gnomad4 OTH
AF:
0.00117

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.64
CADD
Benign
0.020
DANN
Benign
0.30

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
0.00061
dbscSNV1_RF
Benign
0.24
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs147765409; hg19: chr7-142459877; API