chr13-46067331-A-G
Position:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1
The NM_001872.5(CPB2):āc.678T>Cā(p.Asp226=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 1,553,388 control chromosomes in the GnomAD database, including 79,287 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Genomes: š 0.34 ( 9200 hom., cov: 32)
Exomes š: 0.31 ( 70087 hom. )
Consequence
CPB2
NM_001872.5 synonymous
NM_001872.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.967
Genes affected
CPB2 (HGNC:2300): (carboxypeptidase B2) Carboxypeptidases are enzymes that hydrolyze C-terminal peptide bonds. The carboxypeptidase family includes metallo-, serine, and cysteine carboxypeptidases. According to their substrate specificity, these enzymes are referred to as carboxypeptidase A (cleaving aliphatic residues) or carboxypeptidase B (cleaving basic amino residues). The protein encoded by this gene is activated by trypsin and acts on carboxypeptidase B substrates. After thrombin activation, the mature protein downregulates fibrinolysis. Polymorphisms have been described for this gene and its promoter region. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Jun 2013]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.5).
BP6
Variant 13-46067331-A-G is Benign according to our data. Variant chr13-46067331-A-G is described in ClinVar as [Benign]. Clinvar id is 3059117.Status of the report is no_assertion_criteria_provided, 0 stars.
BP7
Synonymous conserved (PhyloP=0.967 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CPB2 | NM_001872.5 | c.678T>C | p.Asp226= | synonymous_variant | 7/11 | ENST00000181383.10 | |
CPB2-AS1 | NR_046226.1 | n.118+14366A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CPB2 | ENST00000181383.10 | c.678T>C | p.Asp226= | synonymous_variant | 7/11 | 1 | NM_001872.5 | P1 | |
CPB2-AS1 | ENST00000663159.1 | n.469+14366A>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.343 AC: 52177AN: 151950Hom.: 9194 Cov.: 32
GnomAD3 genomes
AF:
AC:
52177
AN:
151950
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.313 AC: 78482AN: 250670Hom.: 12676 AF XY: 0.308 AC XY: 41785AN XY: 135512
GnomAD3 exomes
AF:
AC:
78482
AN:
250670
Hom.:
AF XY:
AC XY:
41785
AN XY:
135512
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.312 AC: 436738AN: 1401320Hom.: 70087 Cov.: 25 AF XY: 0.310 AC XY: 217019AN XY: 700450
GnomAD4 exome
AF:
AC:
436738
AN:
1401320
Hom.:
Cov.:
25
AF XY:
AC XY:
217019
AN XY:
700450
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.343 AC: 52215AN: 152068Hom.: 9200 Cov.: 32 AF XY: 0.344 AC XY: 25561AN XY: 74356
GnomAD4 genome
AF:
AC:
52215
AN:
152068
Hom.:
Cov.:
32
AF XY:
AC XY:
25561
AN XY:
74356
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
912
AN:
3474
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
CPB2-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 17, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at