10-100054045-C-T

Variant names:

• chr10-100054045-C-T
• rs7084921
• NM_001308.3:c.1111+302G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001308.3(CPN1):​c.1111+302G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.432 in 152,056 control chromosomes in the GnomAD database, including 15,059 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 0.43 (15059 hom., cov: 32)
• Consequence: CPN1 NM_001308.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.527
• Publications: 39 publications found

Genes affected

CPN1 (HGNC:2312): (carboxypeptidase N subunit 1) Carboxypeptidase N is a plasma metallo-protease that cleaves basic amino acids from the C terminal of peptides and proteins. The enzyme is important in the regulation of peptides like kinins and anaphylatoxins, and has also been known as kininase-1 and anaphylatoxin inactivator. This enzyme is a tetramer comprised of two identical regulatory subunits and two identical catalytic subunits; this gene encodes the catalytic subunit. Mutations in this gene can be associated with angioedema or chronic urticaria resulting from carboxypeptidase N deficiency. [provided by RefSeq, Jul 2008]

CPN1 Gene-Disease associations (from GenCC):

• carboxypeptidase N deficiency

  Inheritance: AR Classification: LIMITED Submitted by: Illumina, G2P

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.537 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001308.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CPN1	NM_001308.3	MANE Select	c.1111+302G>A		intron	N/A	NP_001299.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CPN1	ENST00000370418.8	TSL:1 MANE Select	c.1111+302G>A		intron	N/A	ENSP00000359446.3
	CPN1	ENST00000877015.1		c.1111+302G>A		intron	N/A	ENSP00000547074.1
	CPN1	ENST00000877014.1		c.1099+302G>A		intron	N/A	ENSP00000547073.1

Frequencies

GnomAD3 genomes AF: 0.432 AC: 65635 AN: 151938 Hom.: 15021 Cov.: 32

Gnomad AFR AF: 0.542

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.432 AC: 65731 AN: 152056 Hom.: 15059 Cov.: 32 AF XY: 0.423 AC XY: 31456 AN XY: 74324

African (AFR) AF: 0.543 AC: 22519 AN: 41468

American (AMR) AF: 0.460 AC: 7020 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 1244 AN: 3472

East Asian (EAS) AF: 0.178 AC: 921 AN: 5184

South Asian (SAS) AF: 0.193 AC: 932 AN: 4822

European-Finnish (FIN) AF: 0.298 AC: 3152 AN: 10572

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.417 AC: 28369 AN: 67976

Other (OTH) AF: 0.460 AC: 970 AN: 2110

Alfa AF: 0.419 Hom.: 28906

Bravo AF: 0.454

Asia WGS AF: 0.207 AC: 721 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.39
DANN	Benign	0.44
PhyloP100		-0.53
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: rs7084921; hg19: chr10-101813802;