chr17-50561472-G-A

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_018896.5(CACNA1G):​c.13G>A​(p.Glu5Lys) variant causes a missense change. The variant allele was found at a frequency of 0.00000145 in 1,382,422 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 31)
Exomes 𝑓: 0.0000014 ( 0 hom. )

Consequence

CACNA1G
NM_018896.5 missense

Scores

3
7
9

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.77
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)

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.24011162).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CACNA1GNM_018896.5 linkc.13G>A p.Glu5Lys 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.13G>A p.Glu5Lys missense_variant Exon 1 of 38 1 NM_018896.5 ENSP00000352011.5 O43497-1
CACNA1GENST00000507510.6 linkc.13G>A p.Glu5Lys missense_variant Exon 1 of 37 1 ENSP00000423112.2 O43497-12

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
AF:
0.00000145
AC:
2
AN:
1382422
Hom.:
0
Cov.:
32
AF XY:
0.00000147
AC XY:
1
AN XY:
682282
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:
0.00000185
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.17
BayesDel_addAF
Uncertain
0.12
D
BayesDel_noAF
Uncertain
-0.060
CADD
Uncertain
25
DANN
Uncertain
1.0
DEOGEN2
Benign
0.020
.;.;.;.;T;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;T;.
Eigen
Benign
-0.29
Eigen_PC
Benign
-0.16
FATHMM_MKL
Uncertain
0.92
D
LIST_S2
Pathogenic
0.98
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
0.67
D
MetaRNN
Benign
0.24
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
0.43
D
MutationAssessor
Benign
0.90
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
-1.0
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
0.33
Sift
Uncertain
0.010
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
0.25
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
0.32, 0.21
.;.;.;.;.;B;.;.;.;.;.;.;.;.;.;.;B;.;.;.;.;.;.;.;B;.
Vest4
0.22
MutPred
0.36
Gain of ubiquitination at E5 (P = 0.006);Gain of ubiquitination at E5 (P = 0.006);Gain of ubiquitination at E5 (P = 0.006);Gain of ubiquitination at E5 (P = 0.006);Gain of ubiquitination at E5 (P = 0.006);Gain of ubiquitination at E5 (P = 0.006);Gain of ubiquitination at E5 (P = 0.006);Gain of ubiquitination at E5 (P = 0.006);Gain of ubiquitination at E5 (P = 0.006);Gain of ubiquitination at E5 (P = 0.006);Gain of ubiquitination at E5 (P = 0.006);Gain of ubiquitination at E5 (P = 0.006);Gain of ubiquitination at E5 (P = 0.006);Gain of ubiquitination at E5 (P = 0.006);Gain of ubiquitination at E5 (P = 0.006);Gain of ubiquitination at E5 (P = 0.006);Gain of ubiquitination at E5 (P = 0.006);Gain of ubiquitination at E5 (P = 0.006);Gain of ubiquitination at E5 (P = 0.006);Gain of ubiquitination at E5 (P = 0.006);Gain of ubiquitination at E5 (P = 0.006);Gain of ubiquitination at E5 (P = 0.006);Gain of ubiquitination at E5 (P = 0.006);Gain of ubiquitination at E5 (P = 0.006);Gain of ubiquitination at E5 (P = 0.006);Gain of ubiquitination at E5 (P = 0.006);
MVP
0.62
MPC
1.4
ClinPred
0.71
D
GERP RS
2.6
Varity_R
0.25
gMVP
0.51

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr17-48638833; API