12-2605073-TC-T
Variant names:
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_000719.7(CACNA1C):c.2961-7delC variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000657 in 152,170 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Consequence
CACNA1C
NM_000719.7 splice_region, intron
NM_000719.7 splice_region, intron
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 12-2605073-TC-T is Benign according to our data. Variant chr12-2605073-TC-T is described in ClinVar as [Likely_benign]. Clinvar id is 3688765.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| CACNA1C | NM_000719.7 | c.2961-7delC | splice_region_variant, intron_variant | Intron 22 of 46 | ENST00000399655.6 | NP_000710.5 | ||
| CACNA1C | NM_001167623.2 | c.2961-7delC | splice_region_variant, intron_variant | Intron 22 of 46 | ENST00000399603.6 | NP_001161095.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| CACNA1C | ENST00000399603.6 | c.2961-7delC | splice_region_variant, intron_variant | Intron 22 of 46 | 5 | NM_001167623.2 | ENSP00000382512.1 | |||
| CACNA1C | ENST00000399655.6 | c.2961-7delC | splice_region_variant, intron_variant | Intron 22 of 46 | 1 | NM_000719.7 | ENSP00000382563.1 | |||
| CACNA1C | ENST00000682544.1 | c.3111-7delC | splice_region_variant, intron_variant | Intron 23 of 49 | ENSP00000507184.1 | |||||
| CACNA1C | ENST00000406454.8 | c.2961-7delC | splice_region_variant, intron_variant | Intron 22 of 47 | 5 | ENSP00000385896.3 | ||||
| CACNA1C | ENST00000399634.6 | c.2961-7delC | splice_region_variant, intron_variant | Intron 22 of 46 | 5 | ENSP00000382542.2 | ||||
| CACNA1C | ENST00000683824.1 | c.3126-7delC | splice_region_variant, intron_variant | Intron 23 of 47 | ENSP00000507867.1 | |||||
| CACNA1C | ENST00000347598.9 | c.3021-7delC | splice_region_variant, intron_variant | Intron 23 of 48 | 1 | ENSP00000266376.6 | ||||
| CACNA1C | ENST00000344100.7 | c.2961-7delC | splice_region_variant, intron_variant | Intron 22 of 46 | 1 | ENSP00000341092.3 | ||||
| CACNA1C | ENST00000327702.12 | c.2961-7delC | splice_region_variant, intron_variant | Intron 22 of 47 | 1 | ENSP00000329877.7 | ||||
| CACNA1C | ENST00000399617.6 | c.2961-7delC | splice_region_variant, intron_variant | Intron 22 of 47 | 5 | ENSP00000382526.1 | ||||
| CACNA1C | ENST00000682462.1 | c.3051-7delC | splice_region_variant, intron_variant | Intron 22 of 46 | ENSP00000507105.1 | |||||
| CACNA1C | ENST00000683781.1 | c.3051-7delC | splice_region_variant, intron_variant | Intron 22 of 46 | ENSP00000507434.1 | |||||
| CACNA1C | ENST00000683840.1 | c.3051-7delC | splice_region_variant, intron_variant | Intron 22 of 46 | ENSP00000507612.1 | |||||
| CACNA1C | ENST00000683956.1 | c.3051-7delC | splice_region_variant, intron_variant | Intron 22 of 46 | ENSP00000506882.1 | |||||
| CACNA1C | ENST00000399638.5 | c.2961-7delC | splice_region_variant, intron_variant | Intron 22 of 47 | 1 | ENSP00000382547.1 | ||||
| CACNA1C | ENST00000335762.10 | c.3036-7delC | splice_region_variant, intron_variant | Intron 23 of 47 | 5 | ENSP00000336982.5 | ||||
| CACNA1C | ENST00000399606.5 | c.3021-7delC | splice_region_variant, intron_variant | Intron 23 of 47 | 1 | ENSP00000382515.1 | ||||
| CACNA1C | ENST00000399621.5 | c.2961-7delC | splice_region_variant, intron_variant | Intron 22 of 46 | 1 | ENSP00000382530.1 | ||||
| CACNA1C | ENST00000399637.5 | c.2961-7delC | splice_region_variant, intron_variant | Intron 22 of 46 | 1 | ENSP00000382546.1 | ||||
| CACNA1C | ENST00000402845.7 | c.2961-7delC | splice_region_variant, intron_variant | Intron 22 of 46 | 1 | ENSP00000385724.3 | ||||
| CACNA1C | ENST00000399629.5 | c.2961-7delC | splice_region_variant, intron_variant | Intron 22 of 46 | 1 | ENSP00000382537.1 | ||||
| CACNA1C | ENST00000682336.1 | c.3036-7delC | splice_region_variant, intron_variant | Intron 23 of 46 | ENSP00000507898.1 | |||||
| CACNA1C | ENST00000399591.5 | c.2961-7delC | splice_region_variant, intron_variant | Intron 22 of 45 | 1 | ENSP00000382500.1 | ||||
| CACNA1C | ENST00000399595.5 | c.2961-7delC | splice_region_variant, intron_variant | Intron 22 of 45 | 1 | ENSP00000382504.1 | ||||
| CACNA1C | ENST00000399649.5 | c.2961-7delC | splice_region_variant, intron_variant | Intron 22 of 45 | 1 | ENSP00000382557.1 | ||||
| CACNA1C | ENST00000399597.5 | c.2961-7delC | splice_region_variant, intron_variant | Intron 22 of 46 | 1 | ENSP00000382506.1 | ||||
| CACNA1C | ENST00000399601.5 | c.2961-7delC | splice_region_variant, intron_variant | Intron 22 of 46 | 1 | ENSP00000382510.1 | ||||
| CACNA1C | ENST00000399641.6 | c.2961-7delC | splice_region_variant, intron_variant | Intron 22 of 46 | 1 | ENSP00000382549.1 | ||||
| CACNA1C | ENST00000399644.5 | c.2961-7delC | splice_region_variant, intron_variant | Intron 22 of 46 | 1 | ENSP00000382552.1 | ||||
| CACNA1C | ENST00000682835.1 | c.2961-7delC | splice_region_variant, intron_variant | Intron 22 of 46 | ENSP00000507282.1 | |||||
| CACNA1C | ENST00000683482.1 | c.2952-7delC | splice_region_variant, intron_variant | Intron 22 of 46 | ENSP00000507169.1 | |||||
| CACNA1C | ENST00000682686.1 | c.2961-7delC | splice_region_variant, intron_variant | Intron 22 of 45 | ENSP00000507309.1 | |||||
| CACNA1C | ENST00000480911.6 | n.*1568-7delC | splice_region_variant, intron_variant | Intron 20 of 26 | 5 | ENSP00000437936.2 |
Frequencies
GnomAD3 genomes 0.00000657 AC: 1AN: 152170Hom.: 0 Cov.: 32
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GnomAD4 genome 0.00000657 AC: 1AN: 152170Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74340
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Long QT syndrome Benign:1
Sep 06, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
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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