rs890737

Variant names:

• chr5-175858895-G-A
• rs890737
• ENST00000359546.8:c.-88-19757G>A

Your query was ambiguous. Multiple possible variants found:

• chr5-175858895-G-A
• chr5-175858895-G-T

Variant summary

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

The ENST00000359546.8(CPLX2):​c.-88-19757G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.561 in 152,146 control chromosomes in the GnomAD database, including 24,888 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 0.56 (24888 hom., cov: 33)
• Consequence: CPLX2 ENST00000359546.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.960
• Publications: 2 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.766 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000359546.8. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CPLX2	NM_006650.4		c.-88-19757G>A		intron	N/A	NP_006641.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CPLX2	ENST00000359546.8	TSL:1	c.-88-19757G>A		intron	N/A	ENSP00000352544.4
	CPLX2	ENST00000515502.1	TSL:4	c.-88-19757G>A		intron	N/A	ENSP00000423564.1

Frequencies

GnomAD3 genomes AF: 0.561 AC: 85268 AN: 152028 Hom.: 24873 Cov.: 33

Gnomad AFR AF: 0.421

Gnomad AMI AF: 0.450

Gnomad AMR AF: 0.639

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.786

Gnomad SAS AF: 0.521

Gnomad FIN AF: 0.741

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.598

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.561 AC: 85332 AN: 152146 Hom.: 24888 Cov.: 33 AF XY: 0.569 AC XY: 42353 AN XY: 74384

African (AFR) AF: 0.421 AC: 17466 AN: 41470

American (AMR) AF: 0.639 AC: 9774 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.393 AC: 1366 AN: 3472

East Asian (EAS) AF: 0.786 AC: 4069 AN: 5178

South Asian (SAS) AF: 0.521 AC: 2512 AN: 4822

European-Finnish (FIN) AF: 0.741 AC: 7847 AN: 10592

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.598 AC: 40646 AN: 68000

Other (OTH) AF: 0.538 AC: 1135 AN: 2110

Alfa AF: 0.571 Hom.: 3147

Bravo AF: 0.550

Asia WGS AF: 0.660 AC: 2290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.3
DANN	Benign	0.49
PhyloP100		0.96
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: rs890737; hg19: chr5-175285898;