chr1-181575988-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000367573.7(CACNA1E):​c.513-1778A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.443 in 151,552 control chromosomes in the GnomAD database, including 15,907 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 0.44 ( 15907 hom., cov: 31)

Consequence

CACNA1E
ENST00000367573.7 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0140
Variant links:
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]

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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=-0.91).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.647 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CACNA1ENM_001205293.3 linkuse as main transcriptc.513-1778A>G intron_variant ENST00000367573.7 NP_001192222.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CACNA1EENST00000367573.7 linkuse as main transcriptc.513-1778A>G intron_variant 1 NM_001205293.3 ENSP00000356545 A2Q15878-1

Frequencies

GnomAD3 genomes
AF:
0.443
AC:
67065
AN:
151432
Hom.:
15879
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.287
Gnomad AMI
AF:
0.504
Gnomad AMR
AF:
0.411
Gnomad ASJ
AF:
0.530
Gnomad EAS
AF:
0.665
Gnomad SAS
AF:
0.375
Gnomad FIN
AF:
0.549
Gnomad MID
AF:
0.420
Gnomad NFE
AF:
0.512
Gnomad OTH
AF:
0.413
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.443
AC:
67142
AN:
151552
Hom.:
15907
Cov.:
31
AF XY:
0.449
AC XY:
33237
AN XY:
74034
show subpopulations
Gnomad4 AFR
AF:
0.287
Gnomad4 AMR
AF:
0.410
Gnomad4 ASJ
AF:
0.530
Gnomad4 EAS
AF:
0.666
Gnomad4 SAS
AF:
0.377
Gnomad4 FIN
AF:
0.549
Gnomad4 NFE
AF:
0.512
Gnomad4 OTH
AF:
0.418
Alfa
AF:
0.496
Hom.:
35368
Bravo
AF:
0.426
Asia WGS
AF:
0.468
AC:
1631
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
3.1
DANN
Benign
0.57

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs12135959; hg19: chr1-181545124; API