4-786531-G-A
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Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_006651.4(CPLX1):c.375C>T(p.Pro125=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000276 in 1,451,130 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000028 ( 0 hom. )
Consequence
CPLX1
NM_006651.4 synonymous
NM_006651.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.41
Genes affected
CPLX1 (HGNC:2309): (complexin 1) 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. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.33).
BP6
Variant 4-786531-G-A is Benign according to our data. Variant chr4-786531-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2172736.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-3.41 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CPLX1 | NM_006651.4 | c.375C>T | p.Pro125= | synonymous_variant | 4/4 | ENST00000304062.11 | |
CPLX1 | XM_011513391.2 | c.330C>T | p.Pro110= | synonymous_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CPLX1 | ENST00000304062.11 | c.375C>T | p.Pro125= | synonymous_variant | 4/4 | 1 | NM_006651.4 | P1 | |
CPLX1 | ENST00000505203.1 | c.312C>T | p.Pro104= | synonymous_variant | 5/5 | 2 | |||
CPLX1 | ENST00000504062.1 | c.330C>T | p.Pro110= | synonymous_variant | 3/3 | 3 | |||
CPLX1 | ENST00000506404.1 | n.428C>T | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
GnomAD4 exome AF: 0.00000276 AC: 4AN: 1451130Hom.: 0 Cov.: 36 AF XY: 0.00000277 AC XY: 2AN XY: 721088
GnomAD4 exome
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36
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721088
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GnomAD4 genome Cov.: 33
GnomAD4 genome
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33
Bravo
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Mar 15, 2022 | - - |
Computational scores
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Name
Calibrated prediction
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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