Variant 3-148834543-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2

The NM_001871.3(CPB1):c.193A>G(p.Ser65Gly) variant causes a missense change. The variant allele was found at a frequency of 0.00414 in 1,613,684 control chromosomes in the GnomAD database, including 17 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.0029 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0043 ( 17 hom. )

Consequence

CPB1
NM_001871.3 missense

Scores

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: 6.34

Variant links:

Genes affected

CPB1 (HGNC:2299): (carboxypeptidase B1) Three different procarboxypeptidases A and two different procarboxypeptidases B have been isolated. The B1 and B2 forms differ from each other mainly in isoelectric point. Carboxypeptidase B1 is a highly tissue-specific protein and is a useful serum marker for acute pancreatitis and dysfunction of pancreatic transplants. It is not elevated in pancreatic carcinoma. [provided by RefSeq, Jul 2008]

CPB1 links:

CPB1 (HGNC:):

CPB1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.006259382).

BP6

Variant 3-148834543-A-G is Benign according to our data. Variant chr3-148834543-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 3034026.Status of the report is no_assertion_criteria_provided, 0 stars.

BS2

High Homozygotes in GnomAdExome4 at 17 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CPB1	NM_001871.3 linkuse as main transcript	c.193A>G	p.Ser65Gly	missense_variant	3/11	ENST00000282957.9	NP_001862.2	P15086

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CPB1	ENST00000282957.9 linkuse as main transcript	c.193A>G	p.Ser65Gly	missense_variant	3/11	1	NM_001871.3	ENSP00000282957.4		P15086

Frequencies

GnomAD3 genomes

AF:

0.00294

AC:

448

AN:

152250

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000916

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00216

Gnomad ASJ

AF:

0.00461

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.00497

Gnomad FIN

AF:

0.00160

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00460

Gnomad OTH

AF:

0.00287

GnomAD3 exomes

AF:

0.00332

AC:

835

AN:

251202

Hom.:

AF XY:

0.00354

AC XY:

480

AN XY:

135774

show subpopulations

Gnomad AFR exome

AF:

0.000800

Gnomad AMR exome

AF:

0.00107

Gnomad ASJ exome

AF:

0.00447

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00360

Gnomad FIN exome

AF:

0.00180

Gnomad NFE exome

AF:

0.00505

Gnomad OTH exome

AF:

0.00294

GnomAD4 exome

AF:

0.00426

AC:

6229

AN:

1461316

Hom.:

Cov.:

AF XY:

0.00425

AC XY:

3093

AN XY:

726966

show subpopulations

Gnomad4 AFR exome

AF:

0.000747

Gnomad4 AMR exome

AF:

0.000984

Gnomad4 ASJ exome

AF:

0.00490

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00381

Gnomad4 FIN exome

AF:

0.00213

Gnomad4 NFE exome

AF:

0.00479

Gnomad4 OTH exome

AF:

0.00436

GnomAD4 genome

AF:

0.00294

AC:

448

AN:

152368

Hom.:

Cov.:

AF XY:

0.00267

AC XY:

199

AN XY:

74518

show subpopulations

Gnomad4 AFR

AF:

0.000914

Gnomad4 AMR

AF:

0.00216

Gnomad4 ASJ

AF:

0.00461

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00497

Gnomad4 FIN

AF:

0.00160

Gnomad4 NFE

AF:

0.00460

Gnomad4 OTH

AF:

0.00284

Alfa

AF:

0.00432

Hom.:

Bravo

AF:

0.00278

TwinsUK

AF:

0.00512

AC:

ALSPAC

AF:

0.00519

AC:

ESP6500AA

AF:

0.00136

AC:

ESP6500EA

AF:

0.00407

AC:

ExAC

AF:

0.00362

AC:

439

Asia WGS

AF:

0.00144

AC:

AN:

3478

EpiCase

AF:

0.00475

EpiControl

AF:

0.00362

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

CPB1-related disorder

Benign:1

Likely benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Jun 11, 2019

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.099

BayesDel_addAF

Benign

-0.54

BayesDel_noAF

Benign

-0.55

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.052

T;T;T;T

Eigen

Benign

-0.12

Eigen_PC

Benign

-0.0013

FATHMM_MKL

Pathogenic

0.99

LIST_S2

Benign

0.52

.;T;T;T

M_CAP

Benign

0.0075

MetaRNN

Benign

0.0063

T;T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Uncertain

2.4

M;.;M;.

PrimateAI

Benign

0.30

PROVEAN

Benign

-2.1

N;N;N;N

REVEL

Benign

0.11

Sift

Benign

0.33

T;T;T;D

Sift4G

Benign

0.28

T;T;T;T

Polyphen

0.30

B;.;B;.

Vest4

0.28

MVP

0.50

MPC

0.23

ClinPred

0.032

GERP RS

5.0

Varity_R

0.19

gMVP

0.63

Splicing

Name

Calibrated prediction

Score

Prediction

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over