3-132127049-A-G

Variant names:

• chr3-132127049-A-G
• rs1533747
• ENST00000512055.5:c.-1828-86728T>C

Variant summary

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

The ENST00000512055.5(CPNE4):​c.-1828-86728T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.23 in 152,048 control chromosomes in the GnomAD database, including 4,858 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 0.23 (4858 hom., cov: 32)
• Consequence: CPNE4 ENST00000512055.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0570
• Publications: 2 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.454 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.-1828-86728T>C		intron	N/A	ENSP00000421705.1	Q96A23-1

Frequencies

GnomAD3 genomes AF: 0.230 AC: 34935 AN: 151930 Hom.: 4860 Cov.: 32

Gnomad AFR AF: 0.0903

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.230 AC: 34927 AN: 152048 Hom.: 4858 Cov.: 32 AF XY: 0.231 AC XY: 17128 AN XY: 74300

African (AFR) AF: 0.0902 AC: 3745 AN: 41524

American (AMR) AF: 0.299 AC: 4568 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.306 AC: 1061 AN: 3464

East Asian (EAS) AF: 0.469 AC: 2422 AN: 5162

South Asian (SAS) AF: 0.126 AC: 606 AN: 4822

European-Finnish (FIN) AF: 0.283 AC: 2988 AN: 10556

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.276 AC: 18776 AN: 67944

Other (OTH) AF: 0.244 AC: 516 AN: 2112

Alfa AF: 0.264 Hom.: 3816

Bravo AF: 0.228

Asia WGS AF: 0.235 AC: 819 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.6
DANN	Benign	0.56
PhyloP100		0.057
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: rs1533747; hg19: chr3-131845893;