ENST00000512055.5:c.-1828-51856A>G

Variant names:

• chr3-132092177-T-C
• rs1920001
• ENST00000512055.5:c.-1828-51856A>G

Variant summary

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

The ENST00000512055.5(CPNE4):​c.-1828-51856A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0584 in 152,280 control chromosomes in the GnomAD database, including 458 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 0.058 (458 hom., cov: 32)
• Consequence: CPNE4 ENST00000512055.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.111
• Publications: 0 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 = 0.223 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000512055.5. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CPNE4	ENST00000512055.5	TSL:2	c.-1828-51856A>G		intron	N/A	ENSP00000421705.1

Frequencies

GnomAD3 genomes AF: 0.0585 AC: 8904 AN: 152162 Hom.: 458 Cov.: 32

Gnomad AFR AF: 0.0150

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.0421

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.0655

Gnomad FIN AF: 0.0682

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0530

Gnomad OTH AF: 0.0636

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

GnomAD4 genome AF: 0.0584 AC: 8898 AN: 152280 Hom.: 458 Cov.: 32 AF XY: 0.0607 AC XY: 4516 AN XY: 74446

African (AFR) AF: 0.0149 AC: 621 AN: 41574

American (AMR) AF: 0.136 AC: 2082 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0421 AC: 146 AN: 3472

East Asian (EAS) AF: 0.234 AC: 1211 AN: 5180

South Asian (SAS) AF: 0.0655 AC: 316 AN: 4822

European-Finnish (FIN) AF: 0.0682 AC: 724 AN: 10610

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0530 AC: 3607 AN: 68028

Other (OTH) AF: 0.0629 AC: 133 AN: 2114

Alfa AF: 0.0472 Hom.: 35

Bravo AF: 0.0648

Asia WGS AF: 0.126 AC: 438 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	0.91
DANN	Benign	0.28
PhyloP100		-0.11
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: rs1920001; hg19: chr3-131811021;