chr3-132095056-G-A

Variant names:

• chr3-132095056-G-A
• rs6775745
• ENST00000512055.5:c.-1828-54735C>T

Variant summary

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

The ENST00000512055.5(CPNE4):​c.-1828-54735C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 151,490 control chromosomes in the GnomAD database, including 2,423 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 0.17 (2423 hom., cov: 32)
• Consequence: CPNE4 ENST00000512055.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.91
• Publications: 10 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=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.191 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.-1828-54735C>T		intron_variant	Intron 2 of 19	2		ENSP00000421705.1

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26449 AN: 151390 Hom.: 2420 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.175 AC: 26464 AN: 151490 Hom.: 2423 Cov.: 32 AF XY: 0.174 AC XY: 12873 AN XY: 73958

African (AFR) AF: 0.144 AC: 5949 AN: 41296

American (AMR) AF: 0.143 AC: 2181 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 772 AN: 3462

East Asian (EAS) AF: 0.149 AC: 768 AN: 5142

South Asian (SAS) AF: 0.144 AC: 693 AN: 4808

European-Finnish (FIN) AF: 0.216 AC: 2234 AN: 10322

Middle Eastern (MID) AF: 0.198 AC: 57 AN: 288

European-Non Finnish (NFE) AF: 0.194 AC: 13159 AN: 67898

Other (OTH) AF: 0.194 AC: 410 AN: 2108

Alfa AF: 0.183 Hom.: 8387

Bravo AF: 0.170

Asia WGS AF: 0.161 AC: 559 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	8.2
DANN	Benign	0.72
PhyloP100		1.9
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: rs6775745; hg19: chr3-131813900;