rs11714139

Variant names:

• chr3-132225793-G-A
• rs11714139
• ENST00000512055.5:c.-1829+58250C>T

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CPNE4	ENST00000512055.5	c.-1829+58250C>T		intron_variant	Intron 2 of 19	2		ENSP00000421705.1

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;