rs11724658

Variant names:

• chr4-165372928-G-A
• rs11724658
• ENST00000513982.5:c.-30+11617G>A

Variant summary

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

The ENST00000513982.5(CPE):​c.-30+11617G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 151,894 control chromosomes in the GnomAD database, including 2,316 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 0.16 (2316 hom., cov: 33)
• Consequence: CPE ENST00000513982.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.221

Genes affected

CPE (HGNC:2303): (carboxypeptidase E) This gene encodes a member of the M14 family of metallocarboxypeptidases. The encoded preproprotein is proteolytically processed to generate the mature peptidase. This peripheral membrane protein cleaves C-terminal amino acid residues and is involved in the biosynthesis of peptide hormones and neurotransmitters, including insulin. This protein may also function independently of its peptidase activity, as a neurotrophic factor that promotes neuronal survival, and as a sorting receptor that binds to regulated secretory pathway proteins, including prohormones. Mutations in this gene are implicated in type 2 diabetes. [provided by RefSeq, Nov 2015]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CPE	ENST00000513982.5	c.-30+11617G>A		intron_variant	Intron 1 of 3	4		ENSP00000424830.1

Frequencies

GnomAD3 genomes AF: 0.158 AC: 24042 AN: 151776 Hom.: 2308 Cov.: 33

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.158 AC: 24073 AN: 151894 Hom.: 2316 Cov.: 33 AF XY: 0.155 AC XY: 11496 AN XY: 74230

Gnomad4 AFR AF: 0.268

Gnomad4 AMR AF: 0.125

Gnomad4 ASJ AF: 0.100

Gnomad4 EAS AF: 0.150

Gnomad4 SAS AF: 0.160

Gnomad4 FIN AF: 0.111

Gnomad4 NFE AF: 0.111

Gnomad4 OTH AF: 0.156

Alfa AF: 0.136 Hom.: 276

Bravo AF: 0.163

Asia WGS AF: 0.180 AC: 626 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.83
DANN	Benign	0.88

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11724658; hg19: chr4-166294080;