rs199473660
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 1P and 13B. PP2BP4_StrongBP6BS1BS2
The NM_000719.7(CACNA1C):c.6040G>A(p.Val2014Ile) variant causes a missense change. The variant allele was found at a frequency of 0.000249 in 1,610,992 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.00018 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00026 ( 0 hom. )
Consequence
CACNA1C
NM_000719.7 missense
NM_000719.7 missense
Scores
1
2
13
Clinical Significance
Conservation
PhyloP100: 4.98
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
PP2
Missense variant in gene, where missense usually causes diseases (based on misZ statistic), CACNA1C. . Gene score misZ 6.4654 (greater than the threshold 3.09). Trascript score misZ 7.2674 (greater than threshold 3.09). GenCC has associacion of gene with 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=0.046481907).
BP6
Variant 12-2688702-G-A is Benign according to our data. Variant chr12-2688702-G-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 67556.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=2, Uncertain_significance=6, not_provided=1, Benign=1}. Variant chr12-2688702-G-A is described in Lovd as [Likely_benign].
BS1
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.000184 (28/152282) while in subpopulation SAS AF= 0.00124 (6/4830). AF 95% confidence interval is 0.000541. There are 0 homozygotes in gnomad4. There are 16 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High AC in GnomAd4 at 28 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CACNA1C | NM_000719.7 | c.6040G>A | p.Val2014Ile | missense_variant | 46/47 | ENST00000399655.6 | NP_000710.5 | |
CACNA1C | NM_001167623.2 | c.6040G>A | p.Val2014Ile | missense_variant | 46/47 | ENST00000399603.6 | NP_001161095.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CACNA1C | ENST00000399603.6 | c.6040G>A | p.Val2014Ile | missense_variant | 46/47 | 5 | NM_001167623.2 | ENSP00000382512.1 | ||
CACNA1C | ENST00000399655.6 | c.6040G>A | p.Val2014Ile | missense_variant | 46/47 | 1 | NM_000719.7 | ENSP00000382563.1 | ||
CACNA1C | ENST00000682544.1 | c.6379G>A | p.Val2127Ile | missense_variant | 49/50 | ENSP00000507184.1 | ||||
CACNA1C | ENST00000406454.8 | c.6253G>A | p.Val2085Ile | missense_variant | 47/48 | 5 | ENSP00000385896.3 | |||
CACNA1C | ENST00000399634.6 | c.6220G>A | p.Val2074Ile | missense_variant | 46/47 | 5 | ENSP00000382542.2 | |||
CACNA1C | ENST00000683824.1 | c.6205G>A | p.Val2069Ile | missense_variant | 47/48 | ENSP00000507867.1 | ||||
CACNA1C | ENST00000347598.9 | c.6184G>A | p.Val2062Ile | missense_variant | 48/49 | 1 | ENSP00000266376.6 | |||
CACNA1C | ENST00000344100.7 | c.6163G>A | p.Val2055Ile | missense_variant | 46/47 | 1 | ENSP00000341092.3 | |||
CACNA1C | ENST00000327702.12 | c.6145G>A | p.Val2049Ile | missense_variant | 47/48 | 1 | ENSP00000329877.7 | |||
CACNA1C | ENST00000399617.6 | c.6145G>A | p.Val2049Ile | missense_variant | 47/48 | 5 | ENSP00000382526.1 | |||
CACNA1C | ENST00000682462.1 | c.6130G>A | p.Val2044Ile | missense_variant | 46/47 | ENSP00000507105.1 | ||||
CACNA1C | ENST00000683781.1 | c.6130G>A | p.Val2044Ile | missense_variant | 46/47 | ENSP00000507434.1 | ||||
CACNA1C | ENST00000683840.1 | c.6130G>A | p.Val2044Ile | missense_variant | 46/47 | ENSP00000507612.1 | ||||
CACNA1C | ENST00000683956.1 | c.6130G>A | p.Val2044Ile | missense_variant | 46/47 | ENSP00000506882.1 | ||||
CACNA1C | ENST00000399638.5 | c.6124G>A | p.Val2042Ile | missense_variant | 47/48 | 1 | ENSP00000382547.1 | |||
CACNA1C | ENST00000335762.10 | c.6115G>A | p.Val2039Ile | missense_variant | 47/48 | 5 | ENSP00000336982.5 | |||
CACNA1C | ENST00000399606.5 | c.6100G>A | p.Val2034Ile | missense_variant | 47/48 | 1 | ENSP00000382515.1 | |||
CACNA1C | ENST00000399621.5 | c.6097G>A | p.Val2033Ile | missense_variant | 46/47 | 1 | ENSP00000382530.1 | |||
CACNA1C | ENST00000399637.5 | c.6097G>A | p.Val2033Ile | missense_variant | 46/47 | 1 | ENSP00000382546.1 | |||
CACNA1C | ENST00000402845.7 | c.6097G>A | p.Val2033Ile | missense_variant | 46/47 | 1 | ENSP00000385724.3 | |||
CACNA1C | ENST00000399629.5 | c.6091G>A | p.Val2031Ile | missense_variant | 46/47 | 1 | ENSP00000382537.1 | |||
CACNA1C | ENST00000682336.1 | c.6082G>A | p.Val2028Ile | missense_variant | 46/47 | ENSP00000507898.1 | ||||
CACNA1C | ENST00000399591.5 | c.6064G>A | p.Val2022Ile | missense_variant | 45/46 | 1 | ENSP00000382500.1 | |||
CACNA1C | ENST00000399595.5 | c.6064G>A | p.Val2022Ile | missense_variant | 45/46 | 1 | ENSP00000382504.1 | |||
CACNA1C | ENST00000399649.5 | c.6058G>A | p.Val2020Ile | missense_variant | 45/46 | 1 | ENSP00000382557.1 | |||
CACNA1C | ENST00000399597.5 | c.6040G>A | p.Val2014Ile | missense_variant | 46/47 | 1 | ENSP00000382506.1 | |||
CACNA1C | ENST00000399601.5 | c.6040G>A | p.Val2014Ile | missense_variant | 46/47 | 1 | ENSP00000382510.1 | |||
CACNA1C | ENST00000399641.6 | c.6040G>A | p.Val2014Ile | missense_variant | 46/47 | 1 | ENSP00000382549.1 | |||
CACNA1C | ENST00000399644.5 | c.6040G>A | p.Val2014Ile | missense_variant | 46/47 | 1 | ENSP00000382552.1 | |||
CACNA1C | ENST00000682835.1 | c.6040G>A | p.Val2014Ile | missense_variant | 46/47 | ENSP00000507282.1 | ||||
CACNA1C | ENST00000683482.1 | c.6031G>A | p.Val2011Ile | missense_variant | 46/47 | ENSP00000507169.1 | ||||
CACNA1C | ENST00000682686.1 | c.6007G>A | p.Val2003Ile | missense_variant | 45/46 | ENSP00000507309.1 |
Frequencies
GnomAD3 genomes AF: 0.000184 AC: 28AN: 152164Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000345 AC: 83AN: 240516Hom.: 0 AF XY: 0.000388 AC XY: 51AN XY: 131376
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GnomAD4 exome AF: 0.000256 AC: 373AN: 1458710Hom.: 0 Cov.: 33 AF XY: 0.000274 AC XY: 199AN XY: 725598
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:8Benign:3Other:1
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
not provided Uncertain:3Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Aug 11, 2022 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2024 | CACNA1C: BP4 - |
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Nov 09, 2016 | p.Val2014Ile (GTC>ATC): c.6040 G>A in exon 46 in the CACNA1C gene (NM_000719.6). The V2014I variant was not observed with any significant frequency in approximately 6000 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The V2014I variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is conserved across species. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. A recent publication classifies V2014I as a variant of unknown significance (Dorschner et al., 2013). The variant is found in LQT panel(s). - |
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Mar 11, 2015 | - - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Apr 25, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: 4 papers in HGMD, 3 reference presence in control databases; ExAC: 0.1% (19/13788) South Asian chromosomes - |
CACNA1C-related disorder Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 27, 2024 | The CACNA1C c.6040G>A variant is predicted to result in the amino acid substitution p.Val2014Ile. This variant was reported in individuals with Brugada syndrome (Table1, Burashnikov et al. 2010. PubMed ID: 20817017; Risgaard et al. 2013. PubMed ID: 23414114). This variant is mainly classified as likely benign/uncertain by multiple publications (Table S1, Dorschner et al. 2013. PubMed ID: 24055113; Amendola et al. 2015. PubMed ID: 25637381; Marschall et al. 2019. PubMed ID: 31737537; Maltese et al. 2019. PubMed ID: 31539150 ) and likely pathogenic by one publication (Campuzano et al. 2019. PubMed ID: 30821013). This variant is reported in 0.082% of alleles in individuals of South Asian descent in gnomAD. In ClinVar, this variant has conflicting interpretations of benign, likely benign, and uncertain (https://www.ncbi.nlm.nih.gov/clinvar/variation/67556/?new_evidence=true). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. - |
Brugada syndrome (shorter-than-normal QT interval) Uncertain:1
Uncertain significance, no assertion criteria provided | research | CSER _CC_NCGL, University of Washington | Jun 01, 2014 | - - |
Brugada syndrome 3 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Center For Human Genetics And Laboratory Diagnostics, Dr. Klein, Dr. Rost And Colleagues | Mar 17, 2018 | - - |
Timothy syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Mendelics | May 28, 2019 | - - |
Long QT syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 29, 2024 | - - |
Cardiovascular phenotype Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 10, 2022 | This alteration is classified as 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. - |
Brugada syndrome Other:1
not provided, no classification provided | literature only | Cardiovascular Biomedical Research Unit, Royal Brompton & Harefield NHS Foundation Trust | - | This variant has been reported as associated with Brugada syndrome in the following publications (PMID:20817017). This is a literature report, and does not necessarily reflect the clinical interpretation of the Imperial College / Royal Brompton Cardiovascular Genetics laboratory. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;.;.;.;.;.;.;.;.;.;.;.;.;.;.;T;.;.;.;.;T;.;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Pathogenic
D
M_CAP
Benign
D
MetaRNN
Benign
T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM
Benign
T
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;.
REVEL
Benign
Sift
Benign
T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;D;T;D;D;D;.
Sift4G
Benign
T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
Polyphen
0.53, 0.43, 0.44, 0.18, 0.59, 0.64, 0.76, 0.93, 0.81
.;P;B;B;B;P;P;P;B;P;P;P;P;P;P;.;P;P;.;.;.;P;.
Vest4
MVP
MPC
0.17
ClinPred
T
GERP RS
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at