1-181457774-C-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000524607.6(CACNA1E):c.435-25970C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0935 in 152,242 control chromosomes in the GnomAD database, including 819 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 0.094 ( 819 hom., cov: 33)
Consequence
CACNA1E
ENST00000524607.6 intron
ENST00000524607.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0700
Publications
7 publications found
Genes affected
CACNA1E (HGNC:1392): (calcium voltage-gated channel subunit alpha1 E) Voltage-dependent calcium channels are multisubunit complexes consisting of alpha-1, alpha-2, beta, and delta subunits in a 1:1:1:1 ratio. These channels mediate the entry of calcium ions into excitable cells, and are also involved in a variety of calcium-dependent processes, including muscle contraction, hormone or neurotransmitter release, gene expression, cell motility, cell division and cell death. This gene encodes the alpha-1E subunit of the R-type calcium channels, which belong to the 'high-voltage activated' group that maybe involved in the modulation of firing patterns of neurons important for information processing. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Apr 2011]
CACNA1E Gene-Disease associations (from GenCC):
- developmental and epileptic encephalopathy, 69Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), G2P, Illumina
- genetic developmental and epileptic encephalopathyInheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
- neurodevelopmental disorderInheritance: AD Classification: MODERATE Submitted by: Ambry Genetics
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.71).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.176 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CACNA1E | XM_017002243.2 | c.435-25970C>T | intron_variant | Intron 2 of 49 | XP_016857732.1 | |||
CACNA1E | XM_017002244.2 | c.435-25970C>T | intron_variant | Intron 2 of 49 | XP_016857733.1 | |||
CACNA1E | XM_017002251.1 | c.435-25970C>T | intron_variant | Intron 2 of 49 | XP_016857740.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0936 AC: 14238AN: 152124Hom.: 822 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
14238
AN:
152124
Hom.:
Cov.:
33
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:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0935 AC: 14235AN: 152242Hom.: 819 Cov.: 33 AF XY: 0.0964 AC XY: 7174AN XY: 74432 show subpopulations
GnomAD4 genome
AF:
AC:
14235
AN:
152242
Hom.:
Cov.:
33
AF XY:
AC XY:
7174
AN XY:
74432
show subpopulations
African (AFR)
AF:
AC:
1833
AN:
41540
American (AMR)
AF:
AC:
2389
AN:
15298
Ashkenazi Jewish (ASJ)
AF:
AC:
212
AN:
3472
East Asian (EAS)
AF:
AC:
429
AN:
5184
South Asian (SAS)
AF:
AC:
899
AN:
4822
European-Finnish (FIN)
AF:
AC:
1039
AN:
10600
Middle Eastern (MID)
AF:
AC:
11
AN:
294
European-Non Finnish (NFE)
AF:
AC:
7050
AN:
68010
Other (OTH)
AF:
AC:
205
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
664
1328
1992
2656
3320
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
166
332
498
664
830
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
417
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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