rs11714139

chr3-132225793-G-A

Variant summary

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

The ENST00000512055.5(CPNE4):c.-1829+58250C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 152,208 control chromosomes in the GnomAD database, including 1,128 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 0.12 (1128 hom., cov: 33)
• Consequence: CPNE4 ENST00000512055.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01

Genes affected

CPNE4 (HGNC:2317): (copine 4) This gene belongs to the highly conserved copine family. It encodes a calcium-dependent, phospholipid-binding protein, which may be involved in membrane trafficking, mitogenesis and development. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CPNE4	ENST00000512055.5	c.-1829+58250C>T		intron_variant		2		P1

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17896 AN: 152090 Hom.: 1123 Cov.: 33

Gnomad AFR AF: 0.0830

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.0992

Gnomad ASJ AF: 0.0922

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.118 AC: 17909 AN: 152208 Hom.: 1128 Cov.: 33 AF XY: 0.121 AC XY: 8988 AN XY: 74426

Gnomad4 AFR AF: 0.0831

Gnomad4 AMR AF: 0.0990

Gnomad4 ASJ AF: 0.0922

Gnomad4 EAS AF: 0.169

Gnomad4 SAS AF: 0.168

Gnomad4 FIN AF: 0.189

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.128

Alfa AF: 0.119 Hom.: 1021

Bravo AF: 0.109

Asia WGS AF: 0.182 AC: 633 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	4.3
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11714139; hg19: chr3-131944637;