chr3-131602478-C-T

Position:

• chr3-131602478-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_130808.3(CPNE4):​c.682-14896G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 152,024 control chromosomes in the GnomAD database, including 11,414 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 0.31 (11414 hom., cov: 32)
• Consequence: CPNE4 NM_130808.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.997

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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CPNE4	NM_130808.3	c.682-14896G>A		intron_variant		ENST00000429747.6	NP_570720.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CPNE4	ENST00000429747.6	c.682-14896G>A		intron_variant		1	NM_130808.3	ENSP00000411904	P1

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46479 AN: 151906 Hom.: 11369 Cov.: 32

Gnomad AFR AF: 0.685

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.306 AC: 46577 AN: 152024 Hom.: 11414 Cov.: 32 AF XY: 0.301 AC XY: 22356 AN XY: 74300

Gnomad4 AFR AF: 0.686

Gnomad4 AMR AF: 0.194

Gnomad4 ASJ AF: 0.276

Gnomad4 EAS AF: 0.175

Gnomad4 SAS AF: 0.224

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.147

Gnomad4 OTH AF: 0.275

Alfa AF: 0.179 Hom.: 3785

Bravo AF: 0.326

Asia WGS AF: 0.261 AC: 910 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.5
DANN	Benign	0.56

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs12632185; hg19: chr3-131321322;