rs10876062

chr12-38774384-T-C

Variant summary

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

The NM_153634.3(CPNE8):c.471+1854A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0544 in 152,214 control chromosomes in the GnomAD database, including 527 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 0.054 (527 hom., cov: 32)
• Consequence: CPNE8 NM_153634.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.421

Genes affected

CPNE8 (HGNC:23498): (copine 8) Calcium-dependent membrane-binding proteins may regulate molecular events at the interface of the cell membrane and cytoplasm. This gene is one of several genes that encode a calcium-dependent protein containing two N-terminal type II C2 domains and an integrin A domain-like sequence in the C-terminus. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.356 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CPNE8	NM_153634.3	c.471+1854A>G		intron_variant		ENST00000331366.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CPNE8	ENST00000331366.10	c.471+1854A>G		intron_variant		1	NM_153634.3	P1
CPNE8	ENST00000360449.3	c.435+1854A>G		intron_variant		2
CPNE8	ENST00000550863.1	c.-13+1854A>G		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.0545 AC: 8296 AN: 152096 Hom.: 531 Cov.: 32

Gnomad AFR AF: 0.0129

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.0377

Gnomad ASJ AF: 0.0537

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.0922

Gnomad FIN AF: 0.0356

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0601

Gnomad OTH AF: 0.0645

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

GnomAD4 genome AF: 0.0544 AC: 8284 AN: 152214 Hom.: 527 Cov.: 32 AF XY: 0.0553 AC XY: 4112 AN XY: 74416

Gnomad4 AFR AF: 0.0129

Gnomad4 AMR AF: 0.0377

Gnomad4 ASJ AF: 0.0537

Gnomad4 EAS AF: 0.370

Gnomad4 SAS AF: 0.0919

Gnomad4 FIN AF: 0.0356

Gnomad4 NFE AF: 0.0601

Gnomad4 OTH AF: 0.0639

Alfa AF: 0.0583 Hom.: 446

Bravo AF: 0.0551

Asia WGS AF: 0.196 AC: 678 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	4.1
Dann	Benign	0.76

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: rs10876062; hg19: chr12-39168186;