rs7824873

Positions:

• chr8-86542742-G-A
• chr8-86542742-G-T

Variant summary

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

The NM_003909.5(CPNE3):​c.634-1998G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 151,864 control chromosomes in the GnomAD database, including 1,925 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 0.15 (1925 hom., cov: 32)
• Consequence: CPNE3 NM_003909.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CPNE3	NM_003909.5	c.634-1998G>A		intron_variant		ENST00000517490.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CPNE3	ENST00000517490.6	c.634-1998G>A		intron_variant		1	NM_003909.5	P1
CPNE3	ENST00000517391.5	c.300-1998G>A		intron_variant		3
CPNE3	ENST00000621783.4	c.634-1998G>A		intron_variant		5
CPNE3	ENST00000517862.1	n.61-1998G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23357 AN: 151746 Hom.: 1924 Cov.: 32

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.172

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.0463

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.154 AC: 23374 AN: 151864 Hom.: 1925 Cov.: 32 AF XY: 0.153 AC XY: 11331 AN XY: 74202

Gnomad4 AFR AF: 0.115

Gnomad4 AMR AF: 0.101

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.0465

Gnomad4 SAS AF: 0.145

Gnomad4 FIN AF: 0.223

Gnomad4 NFE AF: 0.187

Gnomad4 OTH AF: 0.134

Alfa AF: 0.114 Hom.: 218

Bravo AF: 0.141

Asia WGS AF: 0.0980 AC: 337 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.14
DANN	Benign	0.57

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: rs7824873; hg19: chr8-87554970; COSMIC: COSV52207055; COSMIC: COSV52207055;