rs1542081

Variant names:

• chr8-86552358-T-C
• rs1542081
• NM_003909.5:c.1120+1124T>C

Variant summary

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

The NM_003909.5(CPNE3):​c.1120+1124T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0977 in 152,220 control chromosomes in the GnomAD database, including 988 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 0.098 (988 hom., cov: 31)
• Consequence: CPNE3 NM_003909.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.281
• Publications: 3 publications found

Genes affected

CPNE3 (HGNC:2316): (copine 3) Calcium-dependent membrane-binding proteins may regulate molecular events at the interface of the cell membrane and cytoplasm. This gene encodes a protein which contains two type II C2 domains in the amino-terminus and an A domain-like sequence in the carboxy-terminus. The A domain mediates interactions between integrins and extracellular ligands. [provided by RefSeq, Aug 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CPNE3	NM_003909.5	c.1120+1124T>C		intron_variant	Intron 14 of 16	ENST00000517490.6	NP_003900.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CPNE3	ENST00000517490.6	c.1120+1124T>C		intron_variant	Intron 14 of 16	1	NM_003909.5	ENSP00000477590.1
CPNE3	ENST00000614678.1	n.706+1124T>C		intron_variant	Intron 4 of 6	1
CPNE3	ENST00000517354.5	n.437+1124T>C		intron_variant	Intron 4 of 4	4

Frequencies

GnomAD3 genomes AF: 0.0978 AC: 14877 AN: 152102 Hom.: 992 Cov.: 31

Gnomad AFR AF: 0.0551

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.0981

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0947

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.0977 AC: 14875 AN: 152220 Hom.: 988 Cov.: 31 AF XY: 0.102 AC XY: 7575 AN XY: 74406

African (AFR) AF: 0.0552 AC: 2294 AN: 41558

American (AMR) AF: 0.0977 AC: 1493 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 463 AN: 3468

East Asian (EAS) AF: 0.337 AC: 1741 AN: 5170

South Asian (SAS) AF: 0.198 AC: 951 AN: 4808

European-Finnish (FIN) AF: 0.105 AC: 1112 AN: 10598

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0947 AC: 6439 AN: 68012

Other (OTH) AF: 0.134 AC: 284 AN: 2112

Alfa AF: 0.0984 Hom.: 892

Bravo AF: 0.0964

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	11
DANN	Benign	0.79
PhyloP100		0.28
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1542081; hg19: chr8-87564586;