rs1920001

Positions:

• chr3-132092177-T-C

Variant summary

Our verdict is Benign. Variant got -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

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CPNE4	ENST00000512055.5	c.-1828-51856A>G		intron_variant		2		ENSP00000421705	P1

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

Gnomad4 AFR AF: 0.0149

Gnomad4 AMR AF: 0.136

Gnomad4 ASJ AF: 0.0421

Gnomad4 EAS AF: 0.234

Gnomad4 SAS AF: 0.0655

Gnomad4 FIN AF: 0.0682

Gnomad4 NFE AF: 0.0530

Gnomad4 OTH AF: 0.0629

Alfa AF: 0.0487 Hom.: 35

Bravo AF: 0.0648

Asia WGS AF: 0.126 AC: 438 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.91
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1920001; hg19: chr3-131811021;