3-132058948-C-T

Variant summary

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

The XR_924489.3(LOC105374111):n.170+3658C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0771 in 152,110 control chromosomes in the GnomAD database, including 707 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 0.077 (707 hom., cov: 32)
• Consequence: LOC105374111 XR_924489.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283

Genes affected

LOC105374111 (HGNC:):

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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374111	XR_924489.3	n.170+3658C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CPNE4	ENST00000512055.5	c.-1828-18627G>A		intron_variant		2		P1

Frequencies

GnomAD3 genomes AF: 0.0771 AC: 11714 AN: 151992 Hom.: 700 Cov.: 32

Gnomad AFR AF: 0.0370

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.0692

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.0764

Gnomad FIN AF: 0.0696

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0665

Gnomad OTH AF: 0.0852

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

GnomAD4 genome AF: 0.0771 AC: 11728 AN: 152110 Hom.: 707 Cov.: 32 AF XY: 0.0785 AC XY: 5841 AN XY: 74366

Gnomad4 AFR AF: 0.0371

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.0692

Gnomad4 EAS AF: 0.249

Gnomad4 SAS AF: 0.0765

Gnomad4 FIN AF: 0.0696

Gnomad4 NFE AF: 0.0665

Gnomad4 OTH AF: 0.0844

Alfa AF: 0.0636 Hom.: 61

Bravo AF: 0.0881

Asia WGS AF: 0.142 AC: 491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.7
Dann	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2951390; hg19: chr3-131777792;