rs938243

chr3-131840730-G-Achr3-131840730-G-C

Variant summary

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

The NM_130808.3(CPNE4):c.180+64534C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.887 in 152,134 control chromosomes in the GnomAD database, including 59,978 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 0.89 (59978 hom., cov: 30)
• Consequence: CPNE4 NM_130808.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.09

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]

LOC105374113 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CPNE4	NM_130808.3	c.180+64534C>T		intron_variant		ENST00000429747.6
LOC105374113	XR_007096089.1	n.189-2678G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CPNE4	ENST00000429747.6	c.180+64534C>T		intron_variant		1	NM_130808.3	P1

Frequencies

GnomAD3 genomes AF: 0.887 AC: 134817 AN: 152014 Hom.: 59938 Cov.: 30

Gnomad AFR AF: 0.827

Gnomad AMI AF: 0.908

Gnomad AMR AF: 0.920

Gnomad ASJ AF: 0.898

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.900

Gnomad FIN AF: 0.915

Gnomad MID AF: 0.857

Gnomad NFE AF: 0.902

Gnomad OTH AF: 0.883

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

GnomAD4 genome AF: 0.887 AC: 134918 AN: 152134 Hom.: 59978 Cov.: 30 AF XY: 0.891 AC XY: 66235 AN XY: 74362

Gnomad4 AFR AF: 0.827

Gnomad4 AMR AF: 0.920

Gnomad4 ASJ AF: 0.898

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.900

Gnomad4 FIN AF: 0.915

Gnomad4 NFE AF: 0.902

Gnomad4 OTH AF: 0.884

Alfa AF: 0.896 Hom.: 57292

Bravo AF: 0.883

Asia WGS AF: 0.952 AC: 3309 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	2.7
Dann	Benign	0.31

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: rs938243; hg19: chr3-131559574;