chr12-38656787-G-A

Variant names:

• chr12-38656787-G-A
• rs2630778
• NM_153634.3:c.1507-2717C>T

Variant summary

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

The NM_153634.3(CPNE8):​c.1507-2717C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 152,150 control chromosomes in the GnomAD database, including 1,383 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 0.12 (1383 hom., cov: 32)
• Consequence: CPNE8 NM_153634.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• Publications: 5 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.225 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CPNE8	NM_153634.3	c.1507-2717C>T		intron_variant	Intron 19 of 19	ENST00000331366.10	NP_705898.1
CPNE8	XM_017018852.2	c.1024-2717C>T		intron_variant	Intron 19 of 19		XP_016874341.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CPNE8	ENST00000331366.10	c.1507-2717C>T		intron_variant	Intron 19 of 19	1	NM_153634.3	ENSP00000329748.5

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18455 AN: 152030 Hom.: 1378 Cov.: 32

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.0978

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.0817

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.0686

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.121 AC: 18471 AN: 152150 Hom.: 1383 Cov.: 32 AF XY: 0.125 AC XY: 9315 AN XY: 74394

African (AFR) AF: 0.165 AC: 6853 AN: 41496

American (AMR) AF: 0.197 AC: 3020 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 575 AN: 3472

East Asian (EAS) AF: 0.236 AC: 1217 AN: 5150

South Asian (SAS) AF: 0.183 AC: 882 AN: 4824

European-Finnish (FIN) AF: 0.0817 AC: 867 AN: 10610

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.0686 AC: 4661 AN: 67990

Other (OTH) AF: 0.122 AC: 257 AN: 2110

Alfa AF: 0.109 Hom.: 516

Bravo AF: 0.132

Asia WGS AF: 0.219 AC: 762 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.1
DANN	Benign	0.50
PhyloP100		0.25
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: rs2630778; hg19: chr12-39050589;