rs7643920

Variant names:

• chr3-132242815-G-A
• rs7643920
• ENST00000512055.5:c.-1829+41228C>T

Variant summary

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

The ENST00000512055.5(CPNE4):​c.-1829+41228C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 152,118 control chromosomes in the GnomAD database, including 3,508 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 (3508 hom., cov: 32)
• Consequence: CPNE4 ENST00000512055.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0740
• Publications: 0 publications found

Genes affected

CPNE4 (HGNC:2317): (copine 4) This gene belongs to the highly conserved copine family. It encodes a calcium-dependent, phospholipid-binding protein, which may be involved in membrane trafficking, mitogenesis and development. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.4 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CPNE4	ENST00000512055.5	c.-1829+41228C>T		intron_variant	Intron 2 of 19	2		ENSP00000421705.1

Frequencies

GnomAD3 genomes AF: 0.125 AC: 18938 AN: 152000 Hom.: 3489 Cov.: 32

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0594

Gnomad ASJ AF: 0.00490

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0681

Gnomad FIN AF: 0.0281

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.00607

Gnomad OTH AF: 0.0988

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

GnomAD4 genome AF: 0.125 AC: 19007 AN: 152118 Hom.: 3508 Cov.: 32 AF XY: 0.121 AC XY: 9020 AN XY: 74360

African (AFR) AF: 0.406 AC: 16817 AN: 41460

American (AMR) AF: 0.0593 AC: 907 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.00490 AC: 17 AN: 3468

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5186

South Asian (SAS) AF: 0.0680 AC: 328 AN: 4826

European-Finnish (FIN) AF: 0.0281 AC: 297 AN: 10566

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.00607 AC: 413 AN: 68004

Other (OTH) AF: 0.0987 AC: 208 AN: 2108

Alfa AF: 0.0879 Hom.: 329

Bravo AF: 0.138

Asia WGS AF: 0.0780 AC: 269 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	13
DANN	Benign	0.80
PhyloP100		0.074
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7643920; hg19: chr3-131961659;