rs10797724

Variant summary

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

The NM_001205293.3(CACNA1E):​c.513-28777A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.733 in 152,120 control chromosomes in the GnomAD database, including 43,234 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 0.73 ( 43234 hom., cov: 32)

Consequence

CACNA1E
NM_001205293.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.413
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=-0.88).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.863 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CACNA1ENM_001205293.3 linkuse as main transcriptc.513-28777A>G intron_variant ENST00000367573.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CACNA1EENST00000367573.7 linkuse as main transcriptc.513-28777A>G intron_variant 1 NM_001205293.3 A2Q15878-1

Frequencies

GnomAD3 genomes
AF:
0.733
AC:
111439
AN:
152002
Hom.:
43225
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.460
Gnomad AMI
AF:
0.939
Gnomad AMR
AF:
0.752
Gnomad ASJ
AF:
0.806
Gnomad EAS
AF:
0.742
Gnomad SAS
AF:
0.717
Gnomad FIN
AF:
0.861
Gnomad MID
AF:
0.775
Gnomad NFE
AF:
0.868
Gnomad OTH
AF:
0.755
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.733
AC:
111476
AN:
152120
Hom.:
43234
Cov.:
32
AF XY:
0.733
AC XY:
54521
AN XY:
74358
show subpopulations
Gnomad4 AFR
AF:
0.459
Gnomad4 AMR
AF:
0.752
Gnomad4 ASJ
AF:
0.806
Gnomad4 EAS
AF:
0.742
Gnomad4 SAS
AF:
0.718
Gnomad4 FIN
AF:
0.861
Gnomad4 NFE
AF:
0.868
Gnomad4 OTH
AF:
0.755
Alfa
AF:
0.829
Hom.:
32882
Bravo
AF:
0.713
Asia WGS
AF:
0.734
AC:
2556
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
6.0
DANN
Benign
0.66

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: rs10797724; hg19: chr1-181518125; API