rs890736

Variant names:

• chr5-175804203-C-A
• rs890736
• ENST00000359546.8:c.-168-4786C>A

Your query was ambiguous. Multiple possible variants found:

• chr5-175804203-C-A
• chr5-175804203-C-G
• chr5-175804203-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000359546.8(CPLX2):​c.-168-4786C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
• Consequence: CPLX2 ENST00000359546.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.657
• Publications: 4 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CPLX2	NM_006650.4	c.-168-4786C>A		intron_variant	Intron 1 of 4		NP_006641.1
CPLX2	XM_005265799.2	c.-89+7419C>A		intron_variant	Intron 1 of 3		XP_005265856.1
CPLX2	XM_047416650.1	c.-346-1241C>A		intron_variant	Intron 1 of 5		XP_047272606.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CPLX2	ENST00000359546.8	c.-168-4786C>A		intron_variant	Intron 1 of 4	1		ENSP00000352544.4
CPLX2	ENST00000515502.1	c.-406-1241C>A		intron_variant	Intron 1 of 4	4		ENSP00000423564.1
CPLX2	ENST00000506642.5	n.158-4786C>A		intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.056
DANN	Benign	0.43
PhyloP100		-0.66

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: rs890736; hg19: chr5-175231206;