rs3822674

Variant names:

• chr5-175880253-T-A
• rs3822674
• NM_001008220.2:c.*208T>A

Your query was ambiguous. Multiple possible variants found:

• chr5-175880253-T-A
• chr5-175880253-T-C

Variant summary

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

The NM_001008220.2(CPLX2):​c.*208T>A variant causes a 3 prime UTR 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: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CPLX2 NM_001008220.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00300
• Publications: 17 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=-0.78).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CPLX2	NM_001008220.2	c.*208T>A		3_prime_UTR_variant	Exon 4 of 4	ENST00000393745.8	NP_001008221.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CPLX2	ENST00000393745.8	c.*208T>A		3_prime_UTR_variant	Exon 4 of 4	1	NM_001008220.2	ENSP00000377346.3
CPLX2	ENST00000359546.8	c.*208T>A		3_prime_UTR_variant	Exon 5 of 5	1		ENSP00000352544.4
CPLX2	ENST00000515094.1	c.*208T>A		downstream_gene_variant		4		ENSP00000421825.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 532618 Hom.: 0 Cov.: 5 AF XY: 0.00 AC XY: 0 AN XY: 287440

African (AFR) AF: 0.00 AC: 0 AN: 14588

American (AMR) AF: 0.00 AC: 0 AN: 31024

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 18362

East Asian (EAS) AF: 0.00 AC: 0 AN: 30274

South Asian (SAS) AF: 0.00 AC: 0 AN: 59348

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 40630

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3884

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 305700

Other (OTH) AF: 0.00 AC: 0 AN: 28808

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	13
DANN	Benign	0.82
PhyloP100		0.0030

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: rs3822674; hg19: chr5-175307256;