rs938243

Variant names:

• chr3-131840730-G-A
• rs938243
• NM_130808.3:c.180+64534C>T

Your query was ambiguous. Multiple possible variants found:

• chr3-131840730-G-A
• chr3-131840730-G-C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 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]

LOC105374113 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CPNE4	NM_130808.3	c.180+64534C>T		intron_variant	Intron 2 of 15	ENST00000429747.6	NP_570720.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CPNE4	ENST00000429747.6	c.180+64534C>T		intron_variant	Intron 2 of 15	1	NM_130808.3	ENSP00000411904.1
CPNE4	ENST00000511604.5	c.180+64534C>T		intron_variant	Intron 5 of 18	1		ENSP00000423811.1

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

African (AFR) AF: 0.827 AC: 34293 AN: 41476

American (AMR) AF: 0.920 AC: 14056 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.898 AC: 3119 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5167 AN: 5174

South Asian (SAS) AF: 0.900 AC: 4333 AN: 4816

European-Finnish (FIN) AF: 0.915 AC: 9689 AN: 10584

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.902 AC: 61317 AN: 68014

Other (OTH) AF: 0.884 AC: 1867 AN: 2112

Alfa AF: 0.894 Hom.: 69877

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
PhyloP100		1.1
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: rs938243; hg19: chr3-131559574;