rs2331406

Variant names:

• chr3-148847695-G-A
• rs2331406
• NM_001871.3:c.981+2069G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001871.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CPB1	NM_001871.3	MANE Select	c.981+2069G>A		intron	N/A	NP_001862.2	P15086

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CPB1	ENST00000282957.9	TSL:1 MANE Select	c.981+2069G>A		intron	N/A	ENSP00000282957.4	P15086
	CPB1	ENST00000491148.5	TSL:5	c.981+2069G>A		intron	N/A	ENSP00000417222.1	P15086
	CPB1	ENST00000968620.1		c.654+2069G>A		intron	N/A	ENSP00000638679.1

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

African (AFR) AF: 0.309 AC: 12814 AN: 41444

American (AMR) AF: 0.177 AC: 2697 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 431 AN: 3464

East Asian (EAS) AF: 0.255 AC: 1319 AN: 5164

South Asian (SAS) AF: 0.284 AC: 1362 AN: 4804

European-Finnish (FIN) AF: 0.236 AC: 2489 AN: 10546

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.223 AC: 15139 AN: 67904

Other (OTH) AF: 0.214 AC: 451 AN: 2112

Alfa AF: 0.229 Hom.: 2168

Bravo AF: 0.239

Asia WGS AF: 0.294 AC: 1022 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.3
DANN	Benign	0.65
PhyloP100		0.0090
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2331406; hg19: chr3-148565482;