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
Consequence
NM_000719.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CACNA1C | NM_000719.7 | c.5150C>G | p.Ala1717Gly | missense_variant | Exon 42 of 47 | ENST00000399655.6 | NP_000710.5 | |
CACNA1C | NM_001167623.2 | c.5150C>G | p.Ala1717Gly | missense_variant | Exon 42 of 47 | ENST00000399603.6 | NP_001161095.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CACNA1C | ENST00000399603.6 | c.5150C>G | p.Ala1717Gly | missense_variant | Exon 42 of 47 | 5 | NM_001167623.2 | ENSP00000382512.1 | ||
CACNA1C | ENST00000399655.6 | c.5150C>G | p.Ala1717Gly | missense_variant | Exon 42 of 47 | 1 | NM_000719.7 | ENSP00000382563.1 | ||
CACNA1C | ENST00000682544.1 | c.5384C>G | p.Ala1795Gly | missense_variant | Exon 44 of 50 | ENSP00000507184.1 | ||||
CACNA1C | ENST00000406454.8 | c.5150C>G | p.Ala1717Gly | missense_variant | Exon 42 of 48 | 5 | ENSP00000385896.3 | |||
CACNA1C | ENST00000399634.6 | c.5117C>G | p.Ala1706Gly | missense_variant | Exon 41 of 47 | 5 | ENSP00000382542.2 | |||
CACNA1C | ENST00000683824.1 | c.5315C>G | p.Ala1772Gly | missense_variant | Exon 43 of 48 | ENSP00000507867.1 | ||||
CACNA1C | ENST00000347598.9 | c.5294C>G | p.Ala1765Gly | missense_variant | Exon 44 of 49 | 1 | ENSP00000266376.6 | |||
CACNA1C | ENST00000344100.7 | c.5273C>G | p.Ala1758Gly | missense_variant | Exon 42 of 47 | 1 | ENSP00000341092.3 | |||
CACNA1C | ENST00000327702.12 | c.5150C>G | p.Ala1717Gly | missense_variant | Exon 42 of 48 | 1 | ENSP00000329877.7 | |||
CACNA1C | ENST00000399617.6 | c.5150C>G | p.Ala1717Gly | missense_variant | Exon 42 of 48 | 5 | ENSP00000382526.1 | |||
CACNA1C | ENST00000682462.1 | c.5240C>G | p.Ala1747Gly | missense_variant | Exon 42 of 47 | ENSP00000507105.1 | ||||
CACNA1C | ENST00000683781.1 | c.5240C>G | p.Ala1747Gly | missense_variant | Exon 42 of 47 | ENSP00000507434.1 | ||||
CACNA1C | ENST00000683840.1 | c.5240C>G | p.Ala1747Gly | missense_variant | Exon 42 of 47 | ENSP00000507612.1 | ||||
CACNA1C | ENST00000683956.1 | c.5240C>G | p.Ala1747Gly | missense_variant | Exon 42 of 47 | ENSP00000506882.1 | ||||
CACNA1C | ENST00000399638.5 | c.5234C>G | p.Ala1745Gly | missense_variant | Exon 43 of 48 | 1 | ENSP00000382547.1 | |||
CACNA1C | ENST00000335762.10 | c.5225C>G | p.Ala1742Gly | missense_variant | Exon 43 of 48 | 5 | ENSP00000336982.5 | |||
CACNA1C | ENST00000399606.5 | c.5210C>G | p.Ala1737Gly | missense_variant | Exon 43 of 48 | 1 | ENSP00000382515.1 | |||
CACNA1C | ENST00000399621.5 | c.5207C>G | p.Ala1736Gly | missense_variant | Exon 42 of 47 | 1 | ENSP00000382530.1 | |||
CACNA1C | ENST00000399637.5 | c.5207C>G | p.Ala1736Gly | missense_variant | Exon 42 of 47 | 1 | ENSP00000382546.1 | |||
CACNA1C | ENST00000402845.7 | c.5207C>G | p.Ala1736Gly | missense_variant | Exon 42 of 47 | 1 | ENSP00000385724.3 | |||
CACNA1C | ENST00000399629.5 | c.5201C>G | p.Ala1734Gly | missense_variant | Exon 42 of 47 | 1 | ENSP00000382537.1 | |||
CACNA1C | ENST00000682336.1 | c.5192C>G | p.Ala1731Gly | missense_variant | Exon 42 of 47 | ENSP00000507898.1 | ||||
CACNA1C | ENST00000399591.5 | c.5174C>G | p.Ala1725Gly | missense_variant | Exon 41 of 46 | 1 | ENSP00000382500.1 | |||
CACNA1C | ENST00000399595.5 | c.5174C>G | p.Ala1725Gly | missense_variant | Exon 41 of 46 | 1 | ENSP00000382504.1 | |||
CACNA1C | ENST00000399649.5 | c.5168C>G | p.Ala1723Gly | missense_variant | Exon 41 of 46 | 1 | ENSP00000382557.1 | |||
CACNA1C | ENST00000399597.5 | c.5150C>G | p.Ala1717Gly | missense_variant | Exon 42 of 47 | 1 | ENSP00000382506.1 | |||
CACNA1C | ENST00000399601.5 | c.5150C>G | p.Ala1717Gly | missense_variant | Exon 42 of 47 | 1 | ENSP00000382510.1 | |||
CACNA1C | ENST00000399641.6 | c.5150C>G | p.Ala1717Gly | missense_variant | Exon 42 of 47 | 1 | ENSP00000382549.1 | |||
CACNA1C | ENST00000399644.5 | c.5150C>G | p.Ala1717Gly | missense_variant | Exon 42 of 47 | 1 | ENSP00000382552.1 | |||
CACNA1C | ENST00000682835.1 | c.5150C>G | p.Ala1717Gly | missense_variant | Exon 42 of 47 | ENSP00000507282.1 | ||||
CACNA1C | ENST00000683482.1 | c.5141C>G | p.Ala1714Gly | missense_variant | Exon 42 of 47 | ENSP00000507169.1 | ||||
CACNA1C | ENST00000682686.1 | c.5117C>G | p.Ala1706Gly | missense_variant | Exon 41 of 46 | ENSP00000507309.1 |
Frequencies
GnomAD3 genomes AF: 0.000499 AC: 76AN: 152196Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000846 AC: 206AN: 243628Hom.: 1 AF XY: 0.000921 AC XY: 122AN XY: 132502
GnomAD4 exome AF: 0.000597 AC: 870AN: 1456958Hom.: 5 Cov.: 31 AF XY: 0.000641 AC XY: 464AN XY: 724114
GnomAD4 genome AF: 0.000499 AC: 76AN: 152314Hom.: 0 Cov.: 33 AF XY: 0.000430 AC XY: 32AN XY: 74478
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:3
Likely benign, criteria provided, single submitter | research | Biesecker Lab/Clinical Genomics Section, National Institutes of Health | Jun 24, 2013 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Feb 06, 2015 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 18, 2021 | This variant is associated with the following publications: (PMID: 22840528, 20817017) - |
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2025 | CACNA1C: BS1, BS2 - |
Long QT syndrome Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | research | Dept of Medical Biology, Uskudar University | Jan 08, 2024 | Criteria: BS1, PP2 - |
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 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 submitter | clinical testing | Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago | Mar 30, 2021 | CACNA1C 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 provided | clinical testing | Blueprint Genetics | Jun 24, 2014 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Mar 18, 2019 | Variant 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 provided | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 16, 2024 | This 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 provided | research | CSER _CC_NCGL, University of Washington | Aug 01, 2016 | Found in patient having exome sequencing for an unrelated indication. No known history of Brugada syndrome. - |
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 28, 2018 | This 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:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at