12-2679743-C-T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7
The NM_000719.7(CACNA1C):c.5391C>T(p.Pro1797Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000691 in 1,448,132 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. Synonymous variant affecting the same amino acid position (i.e. P1797P) has been classified as Likely benign.
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 6.9e-7 ( 0 hom. )
Consequence
CACNA1C
NM_000719.7 synonymous
NM_000719.7 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0290
Publications
0 publications found
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]
ITFG2-AS1 (HGNC:53128): (ITFG2 antisense RNA 1)
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.41).
BP7
Synonymous conserved (PhyloP=0.029 with no splicing effect.
Transcripts
RefSeq
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| CACNA1C | ENST00000399603.6 | c.5391C>T | p.Pro1797Pro | synonymous_variant | Exon 42 of 47 | 5 | NM_001167623.2 | ENSP00000382512.1 | ||
| CACNA1C | ENST00000399655.6 | c.5391C>T | p.Pro1797Pro | synonymous_variant | Exon 42 of 47 | 1 | NM_000719.7 | ENSP00000382563.1 | ||
| CACNA1C | ENST00000682544.1 | c.5625C>T | p.Pro1875Pro | synonymous_variant | Exon 44 of 50 | ENSP00000507184.1 | ||||
| CACNA1C | ENST00000406454.8 | c.5391C>T | p.Pro1797Pro | synonymous_variant | Exon 42 of 48 | 5 | ENSP00000385896.3 | |||
| CACNA1C | ENST00000399634.6 | c.5358C>T | p.Pro1786Pro | synonymous_variant | Exon 41 of 47 | 5 | ENSP00000382542.2 | |||
| CACNA1C | ENST00000683824.1 | c.5556C>T | p.Pro1852Pro | synonymous_variant | Exon 43 of 48 | ENSP00000507867.1 | ||||
| CACNA1C | ENST00000347598.9 | c.5535C>T | p.Pro1845Pro | synonymous_variant | Exon 44 of 49 | 1 | ENSP00000266376.6 | |||
| CACNA1C | ENST00000344100.7 | c.5514C>T | p.Pro1838Pro | synonymous_variant | Exon 42 of 47 | 1 | ENSP00000341092.3 | |||
| CACNA1C | ENST00000327702.12 | c.5391C>T | p.Pro1797Pro | synonymous_variant | Exon 42 of 48 | 1 | ENSP00000329877.7 | |||
| CACNA1C | ENST00000399617.6 | c.5391C>T | p.Pro1797Pro | synonymous_variant | Exon 42 of 48 | 5 | ENSP00000382526.1 | |||
| CACNA1C | ENST00000682462.1 | c.5481C>T | p.Pro1827Pro | synonymous_variant | Exon 42 of 47 | ENSP00000507105.1 | ||||
| CACNA1C | ENST00000683781.1 | c.5481C>T | p.Pro1827Pro | synonymous_variant | Exon 42 of 47 | ENSP00000507434.1 | ||||
| CACNA1C | ENST00000683840.1 | c.5481C>T | p.Pro1827Pro | synonymous_variant | Exon 42 of 47 | ENSP00000507612.1 | ||||
| CACNA1C | ENST00000683956.1 | c.5481C>T | p.Pro1827Pro | synonymous_variant | Exon 42 of 47 | ENSP00000506882.1 | ||||
| CACNA1C | ENST00000399638.5 | c.5475C>T | p.Pro1825Pro | synonymous_variant | Exon 43 of 48 | 1 | ENSP00000382547.1 | |||
| CACNA1C | ENST00000335762.10 | c.5466C>T | p.Pro1822Pro | synonymous_variant | Exon 43 of 48 | 5 | ENSP00000336982.5 | |||
| CACNA1C | ENST00000399606.5 | c.5451C>T | p.Pro1817Pro | synonymous_variant | Exon 43 of 48 | 1 | ENSP00000382515.1 | |||
| CACNA1C | ENST00000399621.5 | c.5448C>T | p.Pro1816Pro | synonymous_variant | Exon 42 of 47 | 1 | ENSP00000382530.1 | |||
| CACNA1C | ENST00000399637.5 | c.5448C>T | p.Pro1816Pro | synonymous_variant | Exon 42 of 47 | 1 | ENSP00000382546.1 | |||
| CACNA1C | ENST00000402845.7 | c.5448C>T | p.Pro1816Pro | synonymous_variant | Exon 42 of 47 | 1 | ENSP00000385724.3 | |||
| CACNA1C | ENST00000399629.5 | c.5442C>T | p.Pro1814Pro | synonymous_variant | Exon 42 of 47 | 1 | ENSP00000382537.1 | |||
| CACNA1C | ENST00000682336.1 | c.5433C>T | p.Pro1811Pro | synonymous_variant | Exon 42 of 47 | ENSP00000507898.1 | ||||
| CACNA1C | ENST00000399591.5 | c.5415C>T | p.Pro1805Pro | synonymous_variant | Exon 41 of 46 | 1 | ENSP00000382500.1 | |||
| CACNA1C | ENST00000399595.5 | c.5415C>T | p.Pro1805Pro | synonymous_variant | Exon 41 of 46 | 1 | ENSP00000382504.1 | |||
| CACNA1C | ENST00000399649.5 | c.5409C>T | p.Pro1803Pro | synonymous_variant | Exon 41 of 46 | 1 | ENSP00000382557.1 | |||
| CACNA1C | ENST00000399597.5 | c.5391C>T | p.Pro1797Pro | synonymous_variant | Exon 42 of 47 | 1 | ENSP00000382506.1 | |||
| CACNA1C | ENST00000399601.5 | c.5391C>T | p.Pro1797Pro | synonymous_variant | Exon 42 of 47 | 1 | ENSP00000382510.1 | |||
| CACNA1C | ENST00000399641.6 | c.5391C>T | p.Pro1797Pro | synonymous_variant | Exon 42 of 47 | 1 | ENSP00000382549.1 | |||
| CACNA1C | ENST00000399644.5 | c.5391C>T | p.Pro1797Pro | synonymous_variant | Exon 42 of 47 | 1 | ENSP00000382552.1 | |||
| CACNA1C | ENST00000682835.1 | c.5391C>T | p.Pro1797Pro | synonymous_variant | Exon 42 of 47 | ENSP00000507282.1 | ||||
| CACNA1C | ENST00000683482.1 | c.5382C>T | p.Pro1794Pro | synonymous_variant | Exon 42 of 47 | ENSP00000507169.1 | ||||
| CACNA1C | ENST00000682686.1 | c.5358C>T | p.Pro1786Pro | synonymous_variant | Exon 41 of 46 | ENSP00000507309.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome AF: 6.91e-7 AC: 1AN: 1448132Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 718866 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
1448132
Hom.:
Cov.:
34
AF XY:
AC XY:
0
AN XY:
718866
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33092
American (AMR)
AF:
AC:
0
AN:
42776
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25792
East Asian (EAS)
AF:
AC:
0
AN:
38944
South Asian (SAS)
AF:
AC:
1
AN:
84334
European-Finnish (FIN)
AF:
AC:
0
AN:
52424
Middle Eastern (MID)
AF:
AC:
0
AN:
5738
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1105162
Other (OTH)
AF:
AC:
0
AN:
59870
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.575
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
33
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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