chr3-132225793-G-A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0831 AC: 3452 AN: 41540

American (AMR) AF: 0.0990 AC: 1515 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0922 AC: 320 AN: 3470

East Asian (EAS) AF: 0.169 AC: 873 AN: 5178

South Asian (SAS) AF: 0.168 AC: 808 AN: 4818

European-Finnish (FIN) AF: 0.189 AC: 1998 AN: 10582

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.125 AC: 8517 AN: 68004

Other (OTH) AF: 0.128 AC: 270 AN: 2114

Alfa AF: 0.118 Hom.: 1374

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
PhyloP100		-2.0
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs11714139; hg19: chr3-131944637;