rs201492706

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 1P and 13B. PP2BP4_StrongBP6BS1BS2

The NM_000719.7(CACNA1C):​c.5150C>G​(p.Ala1717Gly) variant causes a missense change. The variant allele was found at a frequency of 0.000588 in 1,609,272 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A1717T) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.00050 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00060 ( 5 hom. )

Consequence

CACNA1C
NM_000719.7 missense

Scores

3
14

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:4B:8

Conservation

PhyloP100: 3.62
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 -12 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: 7.2674 (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=0.0071842372).
BP6
Variant 12-2679502-C-G is Benign according to our data. Variant chr12-2679502-C-G is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 93411.We mark this variant Likely_benign, oryginal submissions are: {Uncertain_significance=3, Benign=2, Likely_benign=4}. Variant chr12-2679502-C-G is described in Lovd as [Likely_benign].
BS1
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.000499 (76/152314) while in subpopulation AMR AF= 0.00098 (15/15302). AF 95% confidence interval is 0.000604. There are 0 homozygotes in gnomad4. There are 32 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High AC in GnomAd4 at 76 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CACNA1CNM_000719.7 linkc.5150C>G p.Ala1717Gly missense_variant Exon 42 of 47 ENST00000399655.6 NP_000710.5 Q13936-12
CACNA1CNM_001167623.2 linkc.5150C>G p.Ala1717Gly missense_variant Exon 42 of 47 ENST00000399603.6 NP_001161095.1 Q13936-37

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CACNA1CENST00000399603.6 linkc.5150C>G p.Ala1717Gly missense_variant Exon 42 of 47 5 NM_001167623.2 ENSP00000382512.1 Q13936-37
CACNA1CENST00000399655.6 linkc.5150C>G p.Ala1717Gly missense_variant Exon 42 of 47 1 NM_000719.7 ENSP00000382563.1 Q13936-12
CACNA1CENST00000682544.1 linkc.5384C>G p.Ala1795Gly missense_variant Exon 44 of 50 ENSP00000507184.1 A0A804HIR0
CACNA1CENST00000406454.8 linkc.5150C>G p.Ala1717Gly missense_variant Exon 42 of 48 5 ENSP00000385896.3 F5GY28
CACNA1CENST00000399634.6 linkc.5117C>G p.Ala1706Gly missense_variant Exon 41 of 47 5 ENSP00000382542.2 E9PDI6
CACNA1CENST00000683824.1 linkc.5315C>G p.Ala1772Gly missense_variant Exon 43 of 48 ENSP00000507867.1 A0A804HKC4
CACNA1CENST00000347598.9 linkc.5294C>G p.Ala1765Gly missense_variant Exon 44 of 49 1 ENSP00000266376.6 Q13936-11
CACNA1CENST00000344100.7 linkc.5273C>G p.Ala1758Gly missense_variant Exon 42 of 47 1 ENSP00000341092.3 Q13936-14
CACNA1CENST00000327702.12 linkc.5150C>G p.Ala1717Gly missense_variant Exon 42 of 48 1 ENSP00000329877.7 A0A0A0MR67
CACNA1CENST00000399617.6 linkc.5150C>G p.Ala1717Gly missense_variant Exon 42 of 48 5 ENSP00000382526.1 A0A0A0MSA1
CACNA1CENST00000682462.1 linkc.5240C>G p.Ala1747Gly missense_variant Exon 42 of 47 ENSP00000507105.1 A0A804HIJ8
CACNA1CENST00000683781.1 linkc.5240C>G p.Ala1747Gly missense_variant Exon 42 of 47 ENSP00000507434.1 A0A804HJB6
CACNA1CENST00000683840.1 linkc.5240C>G p.Ala1747Gly missense_variant Exon 42 of 47 ENSP00000507612.1 A0A804HJR1
CACNA1CENST00000683956.1 linkc.5240C>G p.Ala1747Gly missense_variant Exon 42 of 47 ENSP00000506882.1 A0A804HI37
CACNA1CENST00000399638.5 linkc.5234C>G p.Ala1745Gly missense_variant Exon 43 of 48 1 ENSP00000382547.1 Q13936-31
CACNA1CENST00000335762.10 linkc.5225C>G p.Ala1742Gly missense_variant Exon 43 of 48 5 ENSP00000336982.5 F5H522
CACNA1CENST00000399606.5 linkc.5210C>G p.Ala1737Gly missense_variant Exon 43 of 48 1 ENSP00000382515.1 Q13936-30
CACNA1CENST00000399621.5 linkc.5207C>G p.Ala1736Gly missense_variant Exon 42 of 47 1 ENSP00000382530.1 Q13936-24
CACNA1CENST00000399637.5 linkc.5207C>G p.Ala1736Gly missense_variant Exon 42 of 47 1 ENSP00000382546.1 Q13936-27
CACNA1CENST00000402845.7 linkc.5207C>G p.Ala1736Gly missense_variant Exon 42 of 47 1 ENSP00000385724.3 Q13936-13
CACNA1CENST00000399629.5 linkc.5201C>G p.Ala1734Gly missense_variant Exon 42 of 47 1 ENSP00000382537.1 Q13936-32
CACNA1CENST00000682336.1 linkc.5192C>G p.Ala1731Gly missense_variant Exon 42 of 47 ENSP00000507898.1 A0A804HKE9
CACNA1CENST00000399591.5 linkc.5174C>G p.Ala1725Gly missense_variant Exon 41 of 46 1 ENSP00000382500.1 Q13936-29
CACNA1CENST00000399595.5 linkc.5174C>G p.Ala1725Gly missense_variant Exon 41 of 46 1 ENSP00000382504.1 Q13936-25
CACNA1CENST00000399649.5 linkc.5168C>G p.Ala1723Gly missense_variant Exon 41 of 46 1 ENSP00000382557.1 Q13936-15
CACNA1CENST00000399597.5 linkc.5150C>G p.Ala1717Gly missense_variant Exon 42 of 47 1 ENSP00000382506.1 Q13936-22
CACNA1CENST00000399601.5 linkc.5150C>G p.Ala1717Gly missense_variant Exon 42 of 47 1 ENSP00000382510.1 Q13936-20
CACNA1CENST00000399641.6 linkc.5150C>G p.Ala1717Gly missense_variant Exon 42 of 47 1 ENSP00000382549.1 Q13936-23
CACNA1CENST00000399644.5 linkc.5150C>G p.Ala1717Gly missense_variant Exon 42 of 47 1 ENSP00000382552.1 Q13936-21
CACNA1CENST00000682835.1 linkc.5150C>G p.Ala1717Gly missense_variant Exon 42 of 47 ENSP00000507282.1 A0A804HIZ0
CACNA1CENST00000683482.1 linkc.5141C>G p.Ala1714Gly missense_variant Exon 42 of 47 ENSP00000507169.1 Q13936-35
CACNA1CENST00000682686.1 linkc.5117C>G p.Ala1706Gly missense_variant Exon 41 of 46 ENSP00000507309.1 Q13936-19

Frequencies

GnomAD3 genomes
AF:
0.000499
AC:
76
AN:
152196
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.000121
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000982
Gnomad ASJ
AF:
0.00432
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000514
Gnomad OTH
AF:
0.00239
GnomAD3 exomes
AF:
0.000846
AC:
206
AN:
243628
Hom.:
1
AF XY:
0.000921
AC XY:
122
AN XY:
132502
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00123
Gnomad ASJ exome
AF:
0.00629
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000629
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000663
Gnomad OTH exome
AF:
0.00168
GnomAD4 exome
AF:
0.000597
AC:
870
AN:
1456958
Hom.:
5
Cov.:
31
AF XY:
0.000641
AC XY:
464
AN XY:
724114
show subpopulations
Gnomad4 AFR exome
AF:
0.000390
Gnomad4 AMR exome
AF:
0.00128
Gnomad4 ASJ exome
AF:
0.00659
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000559
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000410
Gnomad4 OTH exome
AF:
0.00128
GnomAD4 genome
AF:
0.000499
AC:
76
AN:
152314
Hom.:
0
Cov.:
33
AF XY:
0.000430
AC XY:
32
AN XY:
74478
show subpopulations
Gnomad4 AFR
AF:
0.000120
Gnomad4 AMR
AF:
0.000980
Gnomad4 ASJ
AF:
0.00432
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000515
Gnomad4 OTH
AF:
0.00237
Alfa
AF:
0.00107
Hom.:
0
Bravo
AF:
0.000646
TwinsUK
AF:
0.00
AC:
0
ALSPAC
AF:
0.000259
AC:
1
ExAC
AF:
0.000595
AC:
72
Asia WGS
AF:
0.000289
AC:
1
AN:
3478

ClinVar

Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:4Benign:8
Revision: criteria provided, conflicting classifications
LINK: link

Submissions by phenotype

not provided Uncertain:1Benign:3
Likely benign, criteria provided, single submitterresearchBiesecker Lab/Clinical Genomics Section, National Institutes of HealthJun 24, 2013- -
Uncertain significance, criteria provided, single submitterclinical testingEurofins Ntd Llc (ga)Feb 06, 2015- -
Benign, criteria provided, single submitterclinical testingGeneDxJan 18, 2021This variant is associated with the following publications: (PMID: 22840528, 20817017) -
Benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenJan 01, 2025CACNA1C: BS1, BS2 -
Long QT syndrome Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitterresearchDept of Medical Biology, Uskudar UniversityJan 08, 2024Criteria: BS1, PP2 -
Likely benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJan 31, 2025- -
Timothy syndrome;C2678478:Brugada syndrome 3;C5774213:Neurodevelopmental disorder with hypotonia, language delay, and skeletal defects with or without seizures;CN260585:Long qt syndrome 8 Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingCenter for Genomics, Ann and Robert H. Lurie Children's Hospital of ChicagoMar 30, 2021CACNA1C NM_000719.6 exon 42 p.Ala1717Gly (c.5150C>G): This variant has not been reported in the literature but is present in 0.1% (41/34056) of Latino alleles, including 1 homozygote, in the Genome Aggregation Database (http://gnomad.broadinstitute.org/rs201492706). This variant is present in ClinVar, with several labs classifying this variant as Likely Benign (Variation ID:93411). Evolutionary conservation and computational predictive tools suggest that this variant may not impact the protein. In summary, data on this variant suggests that this variant does not cause disease, but requires further evidence. Therefore this variant is classified as Likely Benign. -
Restrictive cardiomyopathy;C0023976:Long QT syndrome Uncertain:1
Uncertain significance, no assertion criteria providedclinical testingBlueprint GeneticsJun 24, 2014- -
not specified Benign:1
Likely benign, criteria provided, single submitterclinical testingWomen's Health and Genetics/Laboratory Corporation of America, LabCorpMar 18, 2019Variant summary: CACNA1C c.5150C>G (p.Ala1717Gly) results in a non-conservative amino acid change located in the Voltage-gated calcium channel subunit alpha, C-terminal of the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.00076 in 272838 control chromosomes in the gnomAD database, including 1 homozygotes. The observed variant frequency is approximately 75.87 fold of the estimated maximal expected allele frequency for a pathogenic variant in CACNA1C causing Arrhythmia phenotype (1e-05), strongly suggesting that the variant is benign. c.5150C>G has been reported in the literature in individuals affected with cardiac phenotypes (Burashnikov_2010, Crotti_2012, Forleo_2017, Kostareva_2016, Wemhoner_2015) however without strong evidence for causality. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Five clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. Based on the evidence outlined above, the variant was classified as likely benign. -
CACNA1C-related disorder Benign:1
Likely benign, no assertion criteria providedclinical testingPreventionGenetics, part of Exact SciencesFeb 16, 2024This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Brugada syndrome Benign:1
Likely benign, no assertion criteria providedresearchCSER _CC_NCGL, University of WashingtonAug 01, 2016Found in patient having exome sequencing for an unrelated indication. No known history of Brugada syndrome. -
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitterclinical testingAmbry GeneticsJun 28, 2018This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
-0.30
T
BayesDel_noAF
Benign
-0.25
CADD
Benign
22
DANN
Uncertain
0.99
DEOGEN2
Benign
0.012
T;.;.;.;.;.;.;.;.;.;.;.;.;.;.;T;.;.;.;.;T;.;T
Eigen
Benign
-0.32
Eigen_PC
Benign
-0.14
FATHMM_MKL
Uncertain
0.92
D
M_CAP
Benign
0.080
D
MetaRNN
Benign
0.0072
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
-0.0047
T
MutationAssessor
Benign
-0.20
.;.;.;.;.;.;.;.;.;.;N;.;.;.;.;.;.;.;.;.;.;.;.
PrimateAI
Benign
0.29
T
PROVEAN
Benign
-1.1
N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;.
REVEL
Benign
0.27
Sift
Benign
0.059
T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;D;T;T;T;D;D;D;.
Sift4G
Benign
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
Polyphen
0.0, 0.026, 0.0040
.;B;B;B;B;B;B;B;B;B;B;B;B;B;B;.;B;B;.;.;.;B;.
Vest4
0.15
MVP
0.59
MPC
0.19
ClinPred
0.021
T
GERP RS
3.7
gMVP
0.43

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: rs201492706; hg19: chr12-2788668; API