chr4-786498-C-G
Position:
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_006651.4(CPLX1):c.*3G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.814 in 1,565,414 control chromosomes in the GnomAD database, including 519,749 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.85 ( 55037 hom., cov: 31)
Exomes 𝑓: 0.81 ( 464712 hom. )
Consequence
CPLX1
NM_006651.4 3_prime_UTR
NM_006651.4 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.911
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
Variant 4-786498-C-G is Benign according to our data. Variant chr4-786498-C-G is described in ClinVar as [Benign]. Clinvar id is 1185526.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.948 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CPLX1 | NM_006651.4 | c.*3G>C | 3_prime_UTR_variant | 4/4 | ENST00000304062.11 | ||
CPLX1 | XM_011513391.2 | c.*3G>C | 3_prime_UTR_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CPLX1 | ENST00000304062.11 | c.*3G>C | 3_prime_UTR_variant | 4/4 | 1 | NM_006651.4 | P1 | ||
CPLX1 | ENST00000505203.1 | c.*3G>C | 3_prime_UTR_variant | 5/5 | 2 | ||||
CPLX1 | ENST00000506404.1 | n.461G>C | non_coding_transcript_exon_variant | 2/2 | 2 | ||||
CPLX1 | ENST00000504062.1 | downstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.848 AC: 128737AN: 151806Hom.: 54994 Cov.: 31
GnomAD3 genomes
AF:
AC:
128737
AN:
151806
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.800 AC: 152446AN: 190548Hom.: 61371 AF XY: 0.802 AC XY: 83058AN XY: 103546
GnomAD3 exomes
AF:
AC:
152446
AN:
190548
Hom.:
AF XY:
AC XY:
83058
AN XY:
103546
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.810 AC: 1144767AN: 1413498Hom.: 464712 Cov.: 43 AF XY: 0.810 AC XY: 565710AN XY: 698354
GnomAD4 exome
AF:
AC:
1144767
AN:
1413498
Hom.:
Cov.:
43
AF XY:
AC XY:
565710
AN XY:
698354
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.848 AC: 128830AN: 151916Hom.: 55037 Cov.: 31 AF XY: 0.848 AC XY: 62946AN XY: 74216
GnomAD4 genome
AF:
AC:
128830
AN:
151916
Hom.:
Cov.:
31
AF XY:
AC XY:
62946
AN XY:
74216
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2795
AN:
3472
ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 17, 2019 | - - |
Developmental and epileptic encephalopathy, 63 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 14, 2021 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at