3-132127049-A-G

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.454 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.-1828-86728T>C		intron_variant	Intron 2 of 19	2		ENSP00000421705.1

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

Gnomad4 AFR AF: 0.0902

Gnomad4 AMR AF: 0.299

Gnomad4 ASJ AF: 0.306

Gnomad4 EAS AF: 0.469

Gnomad4 SAS AF: 0.126

Gnomad4 FIN AF: 0.283

Gnomad4 NFE AF: 0.276

Gnomad4 OTH AF: 0.244

Alfa AF: 0.264 Hom.: 2382

Bravo AF: 0.228

Asia WGS AF: 0.235 AC: 819 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.6
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1533747; hg19: chr3-131845893;