chr12-38737190-T-C

Variant names:

• chr12-38737190-T-C
• rs1352123
• NM_153634.3:c.723-6832A>G

Variant summary

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

The NM_153634.3(CPNE8):​c.723-6832A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.553 in 151,394 control chromosomes in the GnomAD database, including 23,671 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 0.55 (23671 hom., cov: 31)
• Consequence: CPNE8 NM_153634.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.532
• Publications: 4 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.786 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_153634.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CPNE8	NM_153634.3	MANE Select	c.723-6832A>G		intron	N/A	NP_705898.1	Q86YQ8-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CPNE8	ENST00000331366.10	TSL:1 MANE Select	c.723-6832A>G		intron	N/A	ENSP00000329748.5	Q86YQ8-1
	CPNE8	ENST00000360449.3	TSL:2	c.687-6832A>G		intron	N/A	ENSP00000353633.3	E7ENV7
	CPNE8	ENST00000862791.1		c.723-6832A>G		intron	N/A	ENSP00000532850.1

Frequencies

GnomAD3 genomes AF: 0.553 AC: 83653 AN: 151314 Hom.: 23674 Cov.: 31

Gnomad AFR AF: 0.478

Gnomad AMI AF: 0.694

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.805

Gnomad SAS AF: 0.661

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.679

Gnomad NFE AF: 0.566

Gnomad OTH AF: 0.594

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

GnomAD4 genome AF: 0.553 AC: 83665 AN: 151394 Hom.: 23671 Cov.: 31 AF XY: 0.555 AC XY: 41008 AN XY: 73934

African (AFR) AF: 0.478 AC: 19756 AN: 41314

American (AMR) AF: 0.574 AC: 8725 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.668 AC: 2321 AN: 3472

East Asian (EAS) AF: 0.806 AC: 4146 AN: 5144

South Asian (SAS) AF: 0.660 AC: 3169 AN: 4798

European-Finnish (FIN) AF: 0.493 AC: 5142 AN: 10432

Middle Eastern (MID) AF: 0.676 AC: 196 AN: 290

European-Non Finnish (NFE) AF: 0.566 AC: 38343 AN: 67732

Other (OTH) AF: 0.588 AC: 1237 AN: 2102

Alfa AF: 0.433 Hom.: 1237

Bravo AF: 0.551

Asia WGS AF: 0.712 AC: 2466 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.55
PhyloP100		-0.53
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: rs1352123; hg19: chr12-39130992;