rs9834560

Positions:

• chr3-131997261-C-A
• chr3-131997261-C-G

Variant summary

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

The NM_130808.3(CPNE4):​c.-2+37306G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.42 in 151,852 control chromosomes in the GnomAD database, including 13,380 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 0.42 (13380 hom., cov: 31)
• Consequence: CPNE4 NM_130808.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.298

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CPNE4	NM_130808.3	c.-2+37306G>T		intron_variant		ENST00000429747.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CPNE4	ENST00000429747.6	c.-2+37306G>T		intron_variant		1	NM_130808.3	P1

Frequencies

GnomAD3 genomes AF: 0.420 AC: 63688 AN: 151734 Hom.: 13359 Cov.: 31

Gnomad AFR AF: 0.445

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.514

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.420 AC: 63750 AN: 151852 Hom.: 13380 Cov.: 31 AF XY: 0.421 AC XY: 31216 AN XY: 74212

Gnomad4 AFR AF: 0.446

Gnomad4 AMR AF: 0.494

Gnomad4 ASJ AF: 0.352

Gnomad4 EAS AF: 0.515

Gnomad4 SAS AF: 0.381

Gnomad4 FIN AF: 0.370

Gnomad4 NFE AF: 0.393

Gnomad4 OTH AF: 0.441

Alfa AF: 0.403 Hom.: 16488

Bravo AF: 0.433

Asia WGS AF: 0.434 AC: 1510 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	13
DANN	Benign	0.84

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: rs9834560; hg19: chr3-131716105;