Variant 16-75223544-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001906.6(CTRB1):c.412G>A(p.Ala138Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.00022 ( 0 hom., cov: 9)

Exomes 𝑓: 0.00038 ( 6 hom. )

Failed GnomAD Quality Control

Consequence

CTRB1
NM_001906.6 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.779

Variant links:

Genes affected

CTRB1 (HGNC:2521): (chymotrypsinogen B1) This gene encodes a member of the serine protease family of enzymes and forms a principal precursor of the pancreatic proteolytic enzymes. The encoded preproprotein is synthesized in the acinar cells of the pancreas and secreted into the small intestine where it undergoes proteolytic activation to generate a functional enzyme. This CTRB1 gene is located head-to-head with the related CTRB2 gene. Some human populations have an alternate haplotype which inverts a 16.6 Kb region containing portions of intron 1, exon 1, and the upstream sequence of the CTRB1 and CTRB2 genes. In this inversion haplotype exon 1 and flanking sequence is swapped in CTRB1 and CTRB2. This inversion is associated with differential gene expression and increased risk for chronic pancreatitis. The GRCh38 assembly represents the minor allele for SNP rs8048956 of the CTRB1 gene. SNP rs8048956 in intron 1 of the CTRB2 gene is diagnostic for this inversion. This CTRB1 gene encodes distinct isoforms, some or all of which may undergo similar processing to generate the mature protein. [provided by RefSeq, Jan 2021]

CTRB1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.045964688).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CTRB1	NM_001906.6 linkuse as main transcript	c.412G>A	p.Ala138Thr	missense_variant	5/7	ENST00000361017.9	NP_001897.4	P17538
CTRB1	NM_001329190.2 linkuse as main transcript	c.412G>A	p.Ala138Thr	missense_variant	5/6		NP_001316119.1	P17538

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CTRB1	ENST00000361017.9 linkuse as main transcript	c.412G>A	p.Ala138Thr	missense_variant	5/7	1	NM_001906.6	ENSP00000354294.4		P17538
CTRB1	ENST00000495583.1 linkuse as main transcript	c.484G>A	p.Ala162Thr	missense_variant	4/4	2		ENSP00000463301.1		J3QKZ2

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

73216

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.0000454

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000677

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000301

Gnomad OTH

AF:

0.00123

GnomAD3 exomes

AF:

0.000348

AC:

AN:

57520

Hom.:

AF XY:

0.000342

AC XY:

AN XY:

29272

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.000495

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000715

Gnomad OTH exome

AF:

0.000542

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000383

AC:

225

AN:

587742

Hom.:

Cov.:

AF XY:

0.000412

AC XY:

126

AN XY:

305872

show subpopulations

Gnomad4 AFR exome

AF:

0.000115

Gnomad4 AMR exome

AF:

0.000596

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.0000242

Gnomad4 NFE exome

AF:

0.000520

Gnomad4 OTH exome

AF:

0.000463

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000219

AC:

AN:

73216

Hom.:

Cov.:

AF XY:

0.000117

AC XY:

AN XY:

34110

show subpopulations

Gnomad4 AFR

AF:

0.0000454

Gnomad4 AMR

AF:

0.000677

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000301

Gnomad4 OTH

AF:

0.00123

Alfa

AF:

0.0000743

Hom.:

ExAC

AF:

0.0000726

AC:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Oct 17, 2024

The c.412G>A (p.A138T) alteration is located in exon 5 (coding exon 5) of the CTRB1 gene. This alteration results from a G to A substitution at nucleotide position 412, causing the alanine (A) at amino acid position 138 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.14

BayesDel_addAF

Benign

-0.25

BayesDel_noAF

Benign

-0.23

CADD

Benign

DANN

Benign

0.90

DEOGEN2

Benign

0.21

T;.

Eigen

Benign

-1.4

Eigen_PC

Benign

-1.5

FATHMM_MKL

Benign

0.063

LIST_S2

Benign

0.76

T;T

M_CAP

Uncertain

0.21

MetaRNN

Benign

0.046

T;T

MetaSVM

Benign

-0.62

PrimateAI

Uncertain

0.49

PROVEAN

Benign

0.030

N;.

REVEL

Benign

0.22

Sift

Benign

0.048

D;.

Sift4G

Benign

0.51

T;T

Polyphen

0.090

B;.

Vest4

0.28

MutPred

0.62

Loss of sheet (P = 0.0817);.;

MVP

0.20

MPC

1.9

ClinPred

0.035

GERP RS

-3.7

Varity_R

0.068

gMVP

0.47

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