12-2053484-TA-T
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_000719.7(CACNA1C):c.-77delA variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: not found (cov: 31)
Consequence
CACNA1C
NM_000719.7 5_prime_UTR
NM_000719.7 5_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.276
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]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP6
Variant 12-2053484-TA-T is Benign according to our data. Variant chr12-2053484-TA-T is described in ClinVar as [Benign]. Clinvar id is 1241429.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| CACNA1C | NM_000719.7 | c.-77delA | 5_prime_UTR_variant | 1/47 | ENST00000399655.6 | NP_000710.5 | ||
| CACNA1C | NM_001167623.2 | c.-77delA | 5_prime_UTR_variant | 1/47 | ENST00000399603.6 | NP_001161095.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| CACNA1C | ENST00000399603 | c.-77delA | 5_prime_UTR_variant | 1/47 | 5 | NM_001167623.2 | ENSP00000382512.1 | |||
| CACNA1C | ENST00000399655 | c.-77delA | 5_prime_UTR_variant | 1/47 | 1 | NM_000719.7 | ENSP00000382563.1 | |||
| CACNA1C | ENST00000406454 | c.-77delA | 5_prime_UTR_variant | 1/48 | 5 | ENSP00000385896.3 | ||||
| CACNA1C | ENST00000399634 | c.-77delA | 5_prime_UTR_variant | 1/47 | 5 | ENSP00000382542.2 | ||||
| CACNA1C | ENST00000347598 | c.-77delA | 5_prime_UTR_variant | 1/49 | 1 | ENSP00000266376.6 | ||||
| CACNA1C | ENST00000327702 | c.-77delA | 5_prime_UTR_variant | 1/48 | 1 | ENSP00000329877.7 | ||||
| CACNA1C | ENST00000399617 | c.-77delA | 5_prime_UTR_variant | 1/48 | 5 | ENSP00000382526.1 | ||||
| CACNA1C | ENST00000335762 | c.-77delA | 5_prime_UTR_variant | 1/48 | 5 | ENSP00000336982.5 | ||||
| CACNA1C | ENST00000399641 | c.-77delA | 5_prime_UTR_variant | 1/47 | 1 | ENSP00000382549.1 | ||||
| CACNA1C | ENST00000682835 | c.-77delA | 5_prime_UTR_variant | 1/47 | ENSP00000507282.1 | |||||
| CACNA1C | ENST00000683482 | c.-77delA | 5_prime_UTR_variant | 1/47 | ENSP00000507169.1 | |||||
| CACNA1C | ENST00000682544.1 | c.140-61738delA | intron_variant | ENSP00000507184.1 | ||||||
| CACNA1C | ENST00000683824.1 | c.140-61738delA | intron_variant | ENSP00000507867.1 | ||||||
| CACNA1C | ENST00000682462.1 | c.140-61738delA | intron_variant | ENSP00000507105.1 | ||||||
| CACNA1C | ENST00000683781.1 | c.140-61738delA | intron_variant | ENSP00000507434.1 | ||||||
| CACNA1C | ENST00000683840.1 | c.140-61738delA | intron_variant | ENSP00000507612.1 | ||||||
| CACNA1C | ENST00000683956.1 | c.140-61738delA | intron_variant | ENSP00000506882.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
31
GnomAD4 exome Cov.: 33
GnomAD4 exome
Cov.:
33
GnomAD4 genome
GnomAD4 genome
Cov.:
31
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
| Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.