10-18539273-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_201596.3(CACNB2):​c.1532G>C​(p.Arg511Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,838 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: 30)
Exomes š‘“: 6.8e-7 ( 0 hom. )

Consequence

CACNB2
NM_201596.3 missense

Scores

3
6
10

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.53
Variant links:
Genes affected
CACNB2 (HGNC:1402): (calcium voltage-gated channel auxiliary subunit beta 2) This gene encodes a subunit of a voltage-dependent calcium channel protein that is a member of the voltage-gated calcium channel superfamily. The gene product was originally identified as an antigen target in Lambert-Eaton myasthenic syndrome, an autoimmune disorder. Mutations in this gene are associated with Brugada syndrome. Alternatively spliced variants encoding different isoforms have been described. [provided by RefSeq, Feb 2013]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.34986323).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CACNB2NM_201596.3 linkc.1532G>C p.Arg511Pro missense_variant Exon 14 of 14 ENST00000324631.13 NP_963890.2 Q08289-1
CACNB2NM_201590.3 linkc.1370G>C p.Arg457Pro missense_variant Exon 13 of 13 ENST00000377329.10 NP_963884.2 Q08289-3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CACNB2ENST00000324631.13 linkc.1532G>C p.Arg511Pro missense_variant Exon 14 of 14 1 NM_201596.3 ENSP00000320025.8 Q08289-1
CACNB2ENST00000377329.10 linkc.1370G>C p.Arg457Pro missense_variant Exon 13 of 13 1 NM_201590.3 ENSP00000366546.4 Q08289-3

Frequencies

GnomAD3 genomes
Cov.:
30
GnomAD4 exome
AF:
6.84e-7
AC:
1
AN:
1461838
Hom.:
0
Cov.:
31
AF XY:
0.00
AC XY:
0
AN XY:
727224
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:
8.99e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.10
BayesDel_addAF
Pathogenic
0.29
D
BayesDel_noAF
Pathogenic
0.18
CADD
Uncertain
23
DANN
Uncertain
1.0
DEOGEN2
Benign
0.27
T;.;T;.;.;.;T;T;.;.;.;T;.;.
Eigen
Uncertain
0.40
Eigen_PC
Uncertain
0.44
FATHMM_MKL
Uncertain
0.96
D
LIST_S2
Pathogenic
0.98
D;D;D;.;D;D;D;D;D;D;D;D;D;D
M_CAP
Benign
0.034
D
MetaRNN
Benign
0.35
T;T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM
Uncertain
0.091
D
MutationAssessor
Benign
1.8
L;.;.;.;.;.;.;.;.;.;.;.;.;.
PrimateAI
Benign
0.33
T
PROVEAN
Benign
-0.46
N;N;N;.;.;N;.;.;N;N;N;.;N;.
REVEL
Benign
0.28
Sift
Uncertain
0.013
D;D;D;.;.;D;.;.;D;D;D;.;D;.
Sift4G
Benign
0.11
T;T;T;.;.;T;T;T;T;T;T;T;T;.
Polyphen
0.99
D;D;D;.;.;D;.;.;.;P;D;.;.;.
Vest4
0.46
MutPred
0.22
Loss of MoRF binding (P = 0.0288);.;.;.;.;.;.;.;.;.;.;.;.;.;
MVP
0.91
MPC
0.53
ClinPred
0.71
D
GERP RS
5.8
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Varity_R
0.27
gMVP
0.47

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.18
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: chr10-18828202; API