rs136855
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_021096.4(CACNA1I):c.3978+54A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 1,594,494 control chromosomes in the GnomAD database, including 43,491 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 0.26 ( 5619 hom., cov: 32)
Exomes 𝑓: 0.22 ( 37872 hom. )
Consequence
CACNA1I
NM_021096.4 intron
NM_021096.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.08
Genes affected
CACNA1I (HGNC:1396): (calcium voltage-gated channel subunit alpha1 I) This gene encodes the pore-forming alpha subunit of a voltage gated calcium channel. The encoded protein is a member of a subfamily of calcium channels referred to as is a low voltage-activated, T-type, calcium channel. The channel encoded by this protein is characterized by a slower activation and inactivation compared to other T-type calcium channels. This protein may be involved in calcium signaling in neurons. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Oct 2011]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.355 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CACNA1I | NM_021096.4 | c.3978+54A>G | intron_variant | ENST00000402142.4 | |||
CACNA1I | NM_001003406.2 | c.3873+54A>G | intron_variant | ||||
CACNA1I | XM_017029035.3 | c.2124+54A>G | intron_variant | ||||
CACNA1I | XM_017029036.2 | c.2124+54A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CACNA1I | ENST00000402142.4 | c.3978+54A>G | intron_variant | 1 | NM_021096.4 | A2 | |||
CACNA1I | ENST00000401624.5 | c.3978+54A>G | intron_variant | 1 | P4 | ||||
CACNA1I | ENST00000404898.5 | c.3873+54A>G | intron_variant | 1 | A2 | ||||
CACNA1I | ENST00000407673.5 | c.3873+54A>G | intron_variant | 1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.260 AC: 39457AN: 151858Hom.: 5617 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
39457
AN:
151858
Hom.:
Cov.:
32
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:
GnomAD4 exome AF: 0.222 AC: 320848AN: 1442518Hom.: 37872 Cov.: 30 AF XY: 0.220 AC XY: 157487AN XY: 714954
GnomAD4 exome
AF:
AC:
320848
AN:
1442518
Hom.:
Cov.:
30
AF XY:
AC XY:
157487
AN XY:
714954
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: 0.260 AC: 39492AN: 151976Hom.: 5619 Cov.: 32 AF XY: 0.253 AC XY: 18784AN XY: 74264
GnomAD4 genome
?
AF:
AC:
39492
AN:
151976
Hom.:
Cov.:
32
AF XY:
AC XY:
18784
AN XY:
74264
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:
487
AN:
3478
ClinVar
Not reported inComputational 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