rs2243404
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000359546.8(CPLX2):c.-340G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 152,508 control chromosomes in the GnomAD database, including 2,771 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 0.19 ( 2766 hom., cov: 33)
Exomes 𝑓: 0.19 ( 5 hom. )
Consequence
CPLX2
ENST00000359546.8 5_prime_UTR
ENST00000359546.8 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0140
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CPLX2 | NM_006650.4 | c.-340G>A | 5_prime_UTR_variant | 1/5 | |||
CPLX2 | XM_005265799.2 | c.-260G>A | 5_prime_UTR_variant | 1/4 | |||
CPLX2 | XM_047416650.1 | c.-518G>A | 5_prime_UTR_variant | 1/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CPLX2 | ENST00000359546.8 | c.-340G>A | 5_prime_UTR_variant | 1/5 | 1 | P1 | |||
CPLX2 | ENST00000506642.5 | upstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.187 AC: 28471AN: 152138Hom.: 2763 Cov.: 33
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GnomAD4 exome AF: 0.187 AC: 47AN: 252Hom.: 5 Cov.: 0 AF XY: 0.191 AC XY: 36AN XY: 188
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GnomAD4 genome ? AF: 0.187 AC: 28482AN: 152256Hom.: 2766 Cov.: 33 AF XY: 0.185 AC XY: 13808AN XY: 74446
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at