17-50561536-C-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_018896.5(CACNA1G):​c.77C>T​(p.Ser26Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000176 in 1,537,864 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. S26S) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.0000066 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000019 ( 0 hom. )

Consequence

CACNA1G
NM_018896.5 missense

Scores

3
8
8

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.74
Variant links:
Genes affected
CACNA1G (HGNC:1394): (calcium voltage-gated channel subunit alpha1 G) Voltage-sensitive calcium 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 a T-type, low-voltage activated calcium channel. The T-type channels generate currents that are both transient, owing to fast inactivation, and tiny, owing to small conductance. T-type channels are thought to be involved in pacemaker activity, low-threshold calcium spikes, neuronal oscillations and resonance, and rebound burst firing. Many alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Sep 2011]
CACNA1G-AS1 (HGNC:27377): (CACNA1G antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BS2
High AC in GnomAdExome4 at 26 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CACNA1GNM_018896.5 linkc.77C>T p.Ser26Leu missense_variant Exon 1 of 38 ENST00000359106.10 NP_061496.2 O43497-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CACNA1GENST00000359106.10 linkc.77C>T p.Ser26Leu missense_variant Exon 1 of 38 1 NM_018896.5 ENSP00000352011.5 O43497-1
CACNA1GENST00000507510.6 linkc.77C>T p.Ser26Leu missense_variant Exon 1 of 37 1 ENSP00000423112.2 O43497-12

Frequencies

GnomAD3 genomes
AF:
0.00000659
AC:
1
AN:
151770
Hom.:
0
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000147
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.0000188
AC:
26
AN:
1386094
Hom.:
0
Cov.:
32
AF XY:
0.0000190
AC XY:
13
AN XY:
684036
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000232
Gnomad4 OTH exome
AF:
0.0000173
GnomAD4 genome
AF:
0.00000659
AC:
1
AN:
151770
Hom.:
0
Cov.:
31
AF XY:
0.0000135
AC XY:
1
AN XY:
74106
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000147
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.20
BayesDel_addAF
Pathogenic
0.17
D
BayesDel_noAF
Uncertain
0.010
CADD
Uncertain
24
DANN
Uncertain
1.0
DEOGEN2
Benign
0.028
.;.;.;.;T;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;T;.
Eigen
Benign
0.19
Eigen_PC
Benign
0.18
FATHMM_MKL
Uncertain
0.85
D
LIST_S2
Uncertain
0.97
D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
M_CAP
Pathogenic
0.81
D
MetaRNN
Uncertain
0.43
T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM
Uncertain
0.64
D
MutationAssessor
Benign
1.4
L;L;L;L;.;L;L;L;L;L;L;L;L;L;L;L;L;L;L;L;L;L;L;L;L;L
PrimateAI
Pathogenic
0.90
D
PROVEAN
Benign
-1.9
N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N
REVEL
Uncertain
0.45
Sift
Uncertain
0.0010
D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
Sift4G
Benign
0.090
T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
Polyphen
0.90, 1.0, 0.045
.;.;.;.;.;P;.;.;.;.;.;.;.;.;.;.;D;.;.;.;.;.;.;.;B;.
Vest4
0.33
MutPred
0.27
Loss of phosphorylation at S26 (P = 0.0172);Loss of phosphorylation at S26 (P = 0.0172);Loss of phosphorylation at S26 (P = 0.0172);Loss of phosphorylation at S26 (P = 0.0172);Loss of phosphorylation at S26 (P = 0.0172);Loss of phosphorylation at S26 (P = 0.0172);Loss of phosphorylation at S26 (P = 0.0172);Loss of phosphorylation at S26 (P = 0.0172);Loss of phosphorylation at S26 (P = 0.0172);Loss of phosphorylation at S26 (P = 0.0172);Loss of phosphorylation at S26 (P = 0.0172);Loss of phosphorylation at S26 (P = 0.0172);Loss of phosphorylation at S26 (P = 0.0172);Loss of phosphorylation at S26 (P = 0.0172);Loss of phosphorylation at S26 (P = 0.0172);Loss of phosphorylation at S26 (P = 0.0172);Loss of phosphorylation at S26 (P = 0.0172);Loss of phosphorylation at S26 (P = 0.0172);Loss of phosphorylation at S26 (P = 0.0172);Loss of phosphorylation at S26 (P = 0.0172);Loss of phosphorylation at S26 (P = 0.0172);Loss of phosphorylation at S26 (P = 0.0172);Loss of phosphorylation at S26 (P = 0.0172);Loss of phosphorylation at S26 (P = 0.0172);Loss of phosphorylation at S26 (P = 0.0172);Loss of phosphorylation at S26 (P = 0.0172);
MVP
0.86
MPC
1.7
ClinPred
0.87
D
GERP RS
2.8
Varity_R
0.25
gMVP
0.58

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: rs947131228; hg19: chr17-48638897; API