12-2681966-A-G
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBA1
The NM_199460.4(CACNA1C):āc.5605A>Gā(p.Met1869Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.82 in 1,598,268 control chromosomes in the GnomAD database, including 539,546 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/15 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.
Frequency
Consequence
NM_199460.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CACNA1C | ENST00000682544.1 | c.5695A>G | p.Met1899Val | missense_variant | Exon 45 of 50 | ENSP00000507184.1 | ||||
CACNA1C | ENST00000327702.12 | c.5461A>G | p.Met1821Val | missense_variant | Exon 43 of 48 | 1 | ENSP00000329877.7 | |||
CACNA1C | ENST00000399617.6 | c.5461A>G | p.Met1821Val | missense_variant | Exon 43 of 48 | 5 | ENSP00000382526.1 | |||
CACNA1C | ENST00000399603.6 | c.5445-584A>G | intron_variant | Intron 42 of 46 | 5 | NM_001167623.2 | ENSP00000382512.1 | |||
CACNA1C | ENST00000399655.6 | c.5445-584A>G | intron_variant | Intron 42 of 46 | 1 | NM_000719.7 | ENSP00000382563.1 | |||
CACNA1C | ENST00000406454.8 | c.5658-584A>G | intron_variant | Intron 43 of 47 | 5 | ENSP00000385896.3 | ||||
CACNA1C | ENST00000399634.6 | c.5625-584A>G | intron_variant | Intron 42 of 46 | 5 | ENSP00000382542.2 | ||||
CACNA1C | ENST00000683824.1 | c.5610-584A>G | intron_variant | Intron 43 of 47 | ENSP00000507867.1 | |||||
CACNA1C | ENST00000347598.9 | c.5589-584A>G | intron_variant | Intron 44 of 48 | 1 | ENSP00000266376.6 | ||||
CACNA1C | ENST00000344100.7 | c.5568-584A>G | intron_variant | Intron 42 of 46 | 1 | ENSP00000341092.3 | ||||
CACNA1C | ENST00000682462.1 | c.5535-584A>G | intron_variant | Intron 42 of 46 | ENSP00000507105.1 | |||||
CACNA1C | ENST00000683781.1 | c.5535-584A>G | intron_variant | Intron 42 of 46 | ENSP00000507434.1 | |||||
CACNA1C | ENST00000683840.1 | c.5535-584A>G | intron_variant | Intron 42 of 46 | ENSP00000507612.1 | |||||
CACNA1C | ENST00000683956.1 | c.5535-584A>G | intron_variant | Intron 42 of 46 | ENSP00000506882.1 | |||||
CACNA1C | ENST00000399638.5 | c.5529-584A>G | intron_variant | Intron 43 of 47 | 1 | ENSP00000382547.1 | ||||
CACNA1C | ENST00000335762.10 | c.5520-584A>G | intron_variant | Intron 43 of 47 | 5 | ENSP00000336982.5 | ||||
CACNA1C | ENST00000399606.5 | c.5505-584A>G | intron_variant | Intron 43 of 47 | 1 | ENSP00000382515.1 | ||||
CACNA1C | ENST00000399621.5 | c.5502-584A>G | intron_variant | Intron 42 of 46 | 1 | ENSP00000382530.1 | ||||
CACNA1C | ENST00000399637.5 | c.5502-584A>G | intron_variant | Intron 42 of 46 | 1 | ENSP00000382546.1 | ||||
CACNA1C | ENST00000402845.7 | c.5502-584A>G | intron_variant | Intron 42 of 46 | 1 | ENSP00000385724.3 | ||||
CACNA1C | ENST00000399629.5 | c.5496-584A>G | intron_variant | Intron 42 of 46 | 1 | ENSP00000382537.1 | ||||
CACNA1C | ENST00000682336.1 | c.5487-584A>G | intron_variant | Intron 42 of 46 | ENSP00000507898.1 | |||||
CACNA1C | ENST00000399591.5 | c.5469-584A>G | intron_variant | Intron 41 of 45 | 1 | ENSP00000382500.1 | ||||
CACNA1C | ENST00000399595.5 | c.5469-584A>G | intron_variant | Intron 41 of 45 | 1 | ENSP00000382504.1 | ||||
CACNA1C | ENST00000399649.5 | c.5463-584A>G | intron_variant | Intron 41 of 45 | 1 | ENSP00000382557.1 | ||||
CACNA1C | ENST00000399597.5 | c.5445-584A>G | intron_variant | Intron 42 of 46 | 1 | ENSP00000382506.1 | ||||
CACNA1C | ENST00000399601.5 | c.5445-584A>G | intron_variant | Intron 42 of 46 | 1 | ENSP00000382510.1 | ||||
CACNA1C | ENST00000399641.6 | c.5445-584A>G | intron_variant | Intron 42 of 46 | 1 | ENSP00000382549.1 | ||||
CACNA1C | ENST00000399644.5 | c.5445-584A>G | intron_variant | Intron 42 of 46 | 1 | ENSP00000382552.1 | ||||
CACNA1C | ENST00000682835.1 | c.5445-584A>G | intron_variant | Intron 42 of 46 | ENSP00000507282.1 | |||||
CACNA1C | ENST00000683482.1 | c.5436-584A>G | intron_variant | Intron 42 of 46 | ENSP00000507169.1 | |||||
CACNA1C | ENST00000682686.1 | c.5412-584A>G | intron_variant | Intron 41 of 45 | ENSP00000507309.1 |
Frequencies
GnomAD3 genomes AF: 0.803 AC: 121654AN: 151560Hom.: 48901 Cov.: 31
GnomAD3 exomes AF: 0.808 AC: 200689AN: 248502Hom.: 81597 AF XY: 0.812 AC XY: 109703AN XY: 135032
GnomAD4 exome AF: 0.822 AC: 1188724AN: 1446592Hom.: 490616 Cov.: 30 AF XY: 0.823 AC XY: 593161AN XY: 720424
GnomAD4 genome AF: 0.803 AC: 121738AN: 151676Hom.: 48930 Cov.: 31 AF XY: 0.804 AC XY: 59525AN XY: 74078
ClinVar
Submissions by phenotype
not specified Benign:4
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 14, 2011 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Benign, criteria provided, single submitter | research | Biesecker Lab/Clinical Genomics Section, National Institutes of Health | Jun 24, 2013 | - - |
Timothy syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 14, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at