18-59286982-C-T

Variant summary

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

The ENST00000587244.5(CPLX4):c.256-10248G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 152,090 control chromosomes in the GnomAD database, including 4,764 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 0.24 (4764 hom., cov: 32)
• Consequence: CPLX4 ENST00000587244.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.624

Genes affected

CPLX4 (HGNC:24330): (complexin 4) This gene likely encodes a member of the complexin family. The encoded protein may be involved in synaptic vesicle exocytosis. [provided by RefSeq, Jan 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CPLX4	ENST00000587244.5	c.256-10248G>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36916 AN: 151972 Hom.: 4765 Cov.: 32

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.243 AC: 36914 AN: 152090 Hom.: 4764 Cov.: 32 AF XY: 0.247 AC XY: 18372 AN XY: 74312

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.288

Gnomad4 ASJ AF: 0.301

Gnomad4 EAS AF: 0.204

Gnomad4 SAS AF: 0.330

Gnomad4 FIN AF: 0.310

Gnomad4 NFE AF: 0.268

Gnomad4 OTH AF: 0.267

Alfa AF: 0.252 Hom.: 710

Bravo AF: 0.235

Asia WGS AF: 0.277 AC: 962 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.37
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9973180; hg19: chr18-56954214;