12-2681966-A-G

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBA1

The NM_199460.4(CACNA1C):ā€‹c.5605A>Gā€‹(p.Met1869Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.82 in 1,598,268 control chromosomes in the GnomAD database, including 539,546 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/15 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā˜…ā˜…). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.

Frequency

Genomes: š‘“ 0.80 ( 48930 hom., cov: 31)
Exomes š‘“: 0.82 ( 490616 hom. )

Consequence

CACNA1C
NM_199460.4 missense

Scores

15

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: -0.521
Variant links:
Genes affected
CACNA1C (HGNC:1390): (calcium voltage-gated channel subunit alpha1 C) This gene encodes an alpha-1 subunit of a voltage-dependent calcium channel. Calcium channels mediate the influx of calcium ions into the cell upon membrane polarization. The alpha-1 subunit consists of 24 transmembrane segments and forms the pore through which ions pass into the cell. The calcium channel consists of a complex of alpha-1, alpha-2/delta, beta, and gamma subunits in a 1:1:1:1 ratio. There are multiple isoforms of each of these proteins, either encoded by different genes or the result of alternative splicing of transcripts. The protein encoded by this gene binds to and is inhibited by dihydropyridine. Alternative splicing results in many transcript variants encoding different proteins. Some of the predicted proteins may not produce functional ion channel subunits. [provided by RefSeq, Oct 2012]
CACNA1C-AS1 (HGNC:40119): (CACNA1C antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

PP2
Missense variant in the CACNA1C gene, where missense mutations are typically associated with disease (based on misZ statistic). The gene has 45 curated pathogenic missense variants (we use a threshold of 10). The gene has 91 curated benign missense variants. Gene score misZ: 6.4654 (above the threshold of 3.09). Trascript score misZ: 7.225 (above the threshold of 3.09). GenCC associations: The gene is linked to intellectual disability, neurodevelopmental disorder with hypotonia, language delay, and skeletal defects with or without seizures, Brugada syndrome, long QT syndrome, short QT syndrome, long qt syndrome 8, Timothy syndrome, Brugada syndrome 3.
BP4
Computational evidence support a benign effect (MetaRNN=2.4774297E-6).
BP6
Variant 12-2681966-A-G is Benign according to our data. Variant chr12-2681966-A-G is described in ClinVar as [Benign]. Clinvar id is 136639.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-2681966-A-G is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.836 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CACNA1CNM_000719.7 linkc.5445-584A>G intron_variant Intron 42 of 46 ENST00000399655.6 NP_000710.5 Q13936-12
CACNA1CNM_001167623.2 linkc.5445-584A>G intron_variant Intron 42 of 46 ENST00000399603.6 NP_001161095.1 Q13936-37

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CACNA1CENST00000682544.1 linkc.5695A>G p.Met1899Val missense_variant Exon 45 of 50 ENSP00000507184.1 A0A804HIR0
CACNA1CENST00000327702.12 linkc.5461A>G p.Met1821Val missense_variant Exon 43 of 48 1 ENSP00000329877.7 A0A0A0MR67
CACNA1CENST00000399617.6 linkc.5461A>G p.Met1821Val missense_variant Exon 43 of 48 5 ENSP00000382526.1 A0A0A0MSA1
CACNA1CENST00000399603.6 linkc.5445-584A>G intron_variant Intron 42 of 46 5 NM_001167623.2 ENSP00000382512.1 Q13936-37
CACNA1CENST00000399655.6 linkc.5445-584A>G intron_variant Intron 42 of 46 1 NM_000719.7 ENSP00000382563.1 Q13936-12
CACNA1CENST00000406454.8 linkc.5658-584A>G intron_variant Intron 43 of 47 5 ENSP00000385896.3 F5GY28
CACNA1CENST00000399634.6 linkc.5625-584A>G intron_variant Intron 42 of 46 5 ENSP00000382542.2 E9PDI6
CACNA1CENST00000683824.1 linkc.5610-584A>G intron_variant Intron 43 of 47 ENSP00000507867.1 A0A804HKC4
CACNA1CENST00000347598.9 linkc.5589-584A>G intron_variant Intron 44 of 48 1 ENSP00000266376.6 Q13936-11
CACNA1CENST00000344100.7 linkc.5568-584A>G intron_variant Intron 42 of 46 1 ENSP00000341092.3 Q13936-14
CACNA1CENST00000682462.1 linkc.5535-584A>G intron_variant Intron 42 of 46 ENSP00000507105.1 A0A804HIJ8
CACNA1CENST00000683781.1 linkc.5535-584A>G intron_variant Intron 42 of 46 ENSP00000507434.1 A0A804HJB6
CACNA1CENST00000683840.1 linkc.5535-584A>G intron_variant Intron 42 of 46 ENSP00000507612.1 A0A804HJR1
CACNA1CENST00000683956.1 linkc.5535-584A>G intron_variant Intron 42 of 46 ENSP00000506882.1 A0A804HI37
CACNA1CENST00000399638.5 linkc.5529-584A>G intron_variant Intron 43 of 47 1 ENSP00000382547.1 Q13936-31
CACNA1CENST00000335762.10 linkc.5520-584A>G intron_variant Intron 43 of 47 5 ENSP00000336982.5 F5H522
CACNA1CENST00000399606.5 linkc.5505-584A>G intron_variant Intron 43 of 47 1 ENSP00000382515.1 Q13936-30
CACNA1CENST00000399621.5 linkc.5502-584A>G intron_variant Intron 42 of 46 1 ENSP00000382530.1 Q13936-24
CACNA1CENST00000399637.5 linkc.5502-584A>G intron_variant Intron 42 of 46 1 ENSP00000382546.1 Q13936-27
CACNA1CENST00000402845.7 linkc.5502-584A>G intron_variant Intron 42 of 46 1 ENSP00000385724.3 Q13936-13
CACNA1CENST00000399629.5 linkc.5496-584A>G intron_variant Intron 42 of 46 1 ENSP00000382537.1 Q13936-32
CACNA1CENST00000682336.1 linkc.5487-584A>G intron_variant Intron 42 of 46 ENSP00000507898.1 A0A804HKE9
CACNA1CENST00000399591.5 linkc.5469-584A>G intron_variant Intron 41 of 45 1 ENSP00000382500.1 Q13936-29
CACNA1CENST00000399595.5 linkc.5469-584A>G intron_variant Intron 41 of 45 1 ENSP00000382504.1 Q13936-25
CACNA1CENST00000399649.5 linkc.5463-584A>G intron_variant Intron 41 of 45 1 ENSP00000382557.1 Q13936-15
CACNA1CENST00000399597.5 linkc.5445-584A>G intron_variant Intron 42 of 46 1 ENSP00000382506.1 Q13936-22
CACNA1CENST00000399601.5 linkc.5445-584A>G intron_variant Intron 42 of 46 1 ENSP00000382510.1 Q13936-20
CACNA1CENST00000399641.6 linkc.5445-584A>G intron_variant Intron 42 of 46 1 ENSP00000382549.1 Q13936-23
CACNA1CENST00000399644.5 linkc.5445-584A>G intron_variant Intron 42 of 46 1 ENSP00000382552.1 Q13936-21
CACNA1CENST00000682835.1 linkc.5445-584A>G intron_variant Intron 42 of 46 ENSP00000507282.1 A0A804HIZ0
CACNA1CENST00000683482.1 linkc.5436-584A>G intron_variant Intron 42 of 46 ENSP00000507169.1 Q13936-35
CACNA1CENST00000682686.1 linkc.5412-584A>G intron_variant Intron 41 of 45 ENSP00000507309.1 Q13936-19

Frequencies

GnomAD3 genomes
AF:
0.803
AC:
121654
AN:
151560
Hom.:
48901
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.779
Gnomad AMI
AF:
0.632
Gnomad AMR
AF:
0.776
Gnomad ASJ
AF:
0.841
Gnomad EAS
AF:
0.623
Gnomad SAS
AF:
0.858
Gnomad FIN
AF:
0.856
Gnomad MID
AF:
0.779
Gnomad NFE
AF:
0.826
Gnomad OTH
AF:
0.791
GnomAD3 exomes
AF:
0.808
AC:
200689
AN:
248502
Hom.:
81597
AF XY:
0.812
AC XY:
109703
AN XY:
135032
show subpopulations
Gnomad AFR exome
AF:
0.784
Gnomad AMR exome
AF:
0.789
Gnomad ASJ exome
AF:
0.837
Gnomad EAS exome
AF:
0.622
Gnomad SAS exome
AF:
0.855
Gnomad FIN exome
AF:
0.854
Gnomad NFE exome
AF:
0.822
Gnomad OTH exome
AF:
0.812
GnomAD4 exome
AF:
0.822
AC:
1188724
AN:
1446592
Hom.:
490616
Cov.:
30
AF XY:
0.823
AC XY:
593161
AN XY:
720424
show subpopulations
Gnomad4 AFR exome
AF:
0.783
Gnomad4 AMR exome
AF:
0.786
Gnomad4 ASJ exome
AF:
0.836
Gnomad4 EAS exome
AF:
0.599
Gnomad4 SAS exome
AF:
0.855
Gnomad4 FIN exome
AF:
0.850
Gnomad4 NFE exome
AF:
0.829
Gnomad4 OTH exome
AF:
0.814
GnomAD4 genome
AF:
0.803
AC:
121738
AN:
151676
Hom.:
48930
Cov.:
31
AF XY:
0.804
AC XY:
59525
AN XY:
74078
show subpopulations
Gnomad4 AFR
AF:
0.779
Gnomad4 AMR
AF:
0.776
Gnomad4 ASJ
AF:
0.841
Gnomad4 EAS
AF:
0.622
Gnomad4 SAS
AF:
0.858
Gnomad4 FIN
AF:
0.856
Gnomad4 NFE
AF:
0.826
Gnomad4 OTH
AF:
0.792
Alfa
AF:
0.823
Hom.:
19526
Bravo
AF:
0.796
TwinsUK
AF:
0.821
AC:
3043
ALSPAC
AF:
0.815
AC:
3141
ESP6500AA
AF:
0.794
AC:
2489
ESP6500EA
AF:
0.831
AC:
5953
ExAC
AF:
0.806
AC:
97141
Asia WGS
AF:
0.751
AC:
2607
AN:
3478
EpiCase
AF:
0.826
EpiControl
AF:
0.818

ClinVar

Significance: Benign
Submissions summary: Benign:6
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not specified Benign:4
Benign, criteria provided, single submitterclinical testingGeneDxJul 14, 2011This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Benign, no assertion criteria providedclinical testingDiagnostic Laboratory, Department of Genetics, University Medical Center Groningen-- -
Benign, no assertion criteria providedclinical testingClinical Genetics, Academic Medical Center-- -
Benign, criteria provided, single submitterresearchBiesecker Lab/Clinical Genomics Section, National Institutes of HealthJun 24, 2013- -
Timothy syndrome Benign:1
Benign, criteria provided, single submitterclinical testingGenome-Nilou LabJul 14, 2021- -
not provided Benign:1
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
-0.58
T
BayesDel_noAF
Benign
-0.46
CADD
Benign
3.0
DANN
Benign
0.40
DEOGEN2
Benign
0.0045
T;T
Eigen
Benign
-1.6
Eigen_PC
Benign
-1.6
FATHMM_MKL
Benign
0.00019
N
MetaRNN
Benign
0.0000025
T;T
MetaSVM
Benign
-0.97
T
PrimateAI
Benign
0.37
T
PROVEAN
Benign
0.16
N;N
REVEL
Benign
0.24
Sift
Benign
0.56
T;T
Sift4G
Benign
0.52
T;T
Vest4
0.020
ClinPred
0.000018
T
GERP RS
0.91

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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: rs10774053; hg19: chr12-2791132; COSMIC: COSV59768974; COSMIC: COSV59768974; API