chr18-59286982-C-T

Variant names:

• chr18-59286982-C-T
• rs9973180
• ENST00000587244.5:c.256-10248G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CPLX4	ENST00000587244.5	c.256-10248G>A		intron_variant	Intron 2 of 2	1		ENSP00000466304.1

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

African (AFR) AF: 0.150 AC: 6233 AN: 41526

American (AMR) AF: 0.288 AC: 4399 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 1042 AN: 3462

East Asian (EAS) AF: 0.204 AC: 1059 AN: 5182

South Asian (SAS) AF: 0.330 AC: 1587 AN: 4816

European-Finnish (FIN) AF: 0.310 AC: 3260 AN: 10530

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.268 AC: 18241 AN: 68004

Other (OTH) AF: 0.267 AC: 563 AN: 2106

Alfa AF: 0.249 Hom.: 720

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
PhyloP100		-0.62
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: rs9973180; hg19: chr18-56954214;