rs2331406

chr3-148847695-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001871.3(CPB1):c.981+2069G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 151,902 control chromosomes in the GnomAD database, including 4,627 homozygotes. 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: 𝑓 0.24 (4627 hom., cov: 31)
• Consequence: CPB1 NM_001871.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.305 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CPB1	NM_001871.3	c.981+2069G>A		intron_variant		ENST00000282957.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CPB1	ENST00000282957.9	c.981+2069G>A		intron_variant		1	NM_001871.3	P1
CPB1	ENST00000491148.5	c.981+2069G>A		intron_variant		5		P1

Frequencies

GnomAD3 genomes AF: 0.244 AC: 36979 AN: 151784 Hom.: 4617 Cov.: 31

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.213

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.244 AC: 37008 AN: 151902 Hom.: 4627 Cov.: 31 AF XY: 0.241 AC XY: 17923 AN XY: 74236

Gnomad4 AFR AF: 0.309

Gnomad4 AMR AF: 0.177

Gnomad4 ASJ AF: 0.124

Gnomad4 EAS AF: 0.255

Gnomad4 SAS AF: 0.284

Gnomad4 FIN AF: 0.236

Gnomad4 NFE AF: 0.223

Gnomad4 OTH AF: 0.214

Alfa AF: 0.230 Hom.: 1944

Bravo AF: 0.239

Asia WGS AF: 0.294 AC: 1022 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	1.3
Dann	Benign	0.65

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

Other links and lift over

dbSNP: rs2331406; hg19: chr3-148565482;