3-132058948-C-T

Variant names:

• chr3-132058948-C-T
• rs2951390
• ENST00000512055.5:c.-1828-18627G>A

Variant summary

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

The ENST00000512055.5(CPNE4):​c.-1828-18627G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0771 in 152,110 control chromosomes in the GnomAD database, including 707 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 0.077 (707 hom., cov: 32)
• Consequence: CPNE4 ENST00000512055.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283
• Publications: 1 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]

LOC105374111 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.238 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CPNE4	ENST00000512055.5	TSL:2	c.-1828-18627G>A		intron	N/A	ENSP00000421705.1	Q96A23-1

Frequencies

GnomAD3 genomes AF: 0.0771 AC: 11714 AN: 151992 Hom.: 700 Cov.: 32

Gnomad AFR AF: 0.0370

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.0692

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.0764

Gnomad FIN AF: 0.0696

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0665

Gnomad OTH AF: 0.0852

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

GnomAD4 genome AF: 0.0771 AC: 11728 AN: 152110 Hom.: 707 Cov.: 32 AF XY: 0.0785 AC XY: 5841 AN XY: 74366

African (AFR) AF: 0.0371 AC: 1541 AN: 41524

American (AMR) AF: 0.178 AC: 2717 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0692 AC: 240 AN: 3468

East Asian (EAS) AF: 0.249 AC: 1287 AN: 5170

South Asian (SAS) AF: 0.0765 AC: 369 AN: 4824

European-Finnish (FIN) AF: 0.0696 AC: 736 AN: 10582

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0665 AC: 4518 AN: 67964

Other (OTH) AF: 0.0844 AC: 178 AN: 2110

Alfa AF: 0.0636 Hom.: 61

Bravo AF: 0.0881

Asia WGS AF: 0.142 AC: 491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.18
PhyloP100		-0.28
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: rs2951390; hg19: chr3-131777792;