chr5-175855307-G-T

Variant names:

• chr5-175855307-G-T
• rs871853
• ENST00000359546.8:c.-88-23345G>T

Variant summary

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

The NM_006650.4(CPLX2):​c.-88-23345G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.691 in 152,142 control chromosomes in the GnomAD database, including 36,891 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 0.69 (36891 hom., cov: 33)
• Consequence: CPLX2 NM_006650.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.46
• Publications: 5 publications found

Genes affected

CPLX2 (HGNC:2310): (complexin 2) Proteins encoded by the complexin/synaphin gene family are cytosolic proteins that function in synaptic vesicle exocytosis. These proteins bind syntaxin, part of the SNAP receptor. The protein product of this gene binds to the SNAP receptor complex and disrupts it, allowing transmitter release. Two transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.931 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006650.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CPLX2	NM_006650.4		c.-88-23345G>T		intron	N/A	NP_006641.1	Q6PUV4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CPLX2	ENST00000359546.8	TSL:1	c.-88-23345G>T		intron	N/A	ENSP00000352544.4	Q6PUV4
	CPLX2	ENST00000899625.1		c.-88-23345G>T		intron	N/A	ENSP00000569684.1
	CPLX2	ENST00000899626.1		c.-88-23345G>T		intron	N/A	ENSP00000569685.1

Frequencies

GnomAD3 genomes AF: 0.691 AC: 105056 AN: 152026 Hom.: 36848 Cov.: 33

Gnomad AFR AF: 0.749

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.716

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.952

Gnomad SAS AF: 0.655

Gnomad FIN AF: 0.747

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.637

Gnomad OTH AF: 0.654

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

GnomAD4 genome AF: 0.691 AC: 105160 AN: 152142 Hom.: 36891 Cov.: 33 AF XY: 0.698 AC XY: 51886 AN XY: 74386

African (AFR) AF: 0.749 AC: 31084 AN: 41490

American (AMR) AF: 0.716 AC: 10946 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.541 AC: 1879 AN: 3470

East Asian (EAS) AF: 0.953 AC: 4937 AN: 5182

South Asian (SAS) AF: 0.655 AC: 3158 AN: 4820

European-Finnish (FIN) AF: 0.747 AC: 7904 AN: 10588

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.637 AC: 43286 AN: 67984

Other (OTH) AF: 0.656 AC: 1387 AN: 2114

Alfa AF: 0.669 Hom.: 5765

Bravo AF: 0.694

Asia WGS AF: 0.789 AC: 2743 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.029
DANN	Benign	0.53
PhyloP100		-2.5
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: rs871853; hg19: chr5-175282310;