rs198550
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_018896.5(CACNA1G):c.1141-29A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.558 in 1,575,772 control chromosomes in the GnomAD database, including 250,866 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.59 ( 26971 hom., cov: 32)
Exomes 𝑓: 0.55 ( 223895 hom. )
Consequence
CACNA1G
NM_018896.5 intron
NM_018896.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.81
Genes affected
CACNA1G (HGNC:1394): (calcium voltage-gated channel subunit alpha1 G) Voltage-sensitive calcium channels mediate the entry of calcium ions into excitable cells, and are also involved in a variety of calcium-dependent processes, including muscle contraction, hormone or neurotransmitter release, gene expression, cell motility, cell division, and cell death. This gene encodes a T-type, low-voltage activated calcium channel. The T-type channels generate currents that are both transient, owing to fast inactivation, and tiny, owing to small conductance. T-type channels are thought to be involved in pacemaker activity, low-threshold calcium spikes, neuronal oscillations and resonance, and rebound burst firing. Many alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Sep 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
?
Variant 17-50575514-A-G is Benign according to our data. Variant chr17-50575514-A-G is described in ClinVar as [Benign]. Clinvar id is 1192603.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.913 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CACNA1G | NM_018896.5 | c.1141-29A>G | intron_variant | ENST00000359106.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CACNA1G | ENST00000359106.10 | c.1141-29A>G | intron_variant | 1 | NM_018896.5 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.588 AC: 89291AN: 151950Hom.: 26924 Cov.: 32
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GnomAD3 exomes AF: 0.600 AC: 133853AN: 222978Hom.: 41433 AF XY: 0.598 AC XY: 72110AN XY: 120682
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GnomAD4 exome AF: 0.554 AC: 789265AN: 1423704Hom.: 223895 Cov.: 35 AF XY: 0.557 AC XY: 391411AN XY: 702558
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GnomAD4 genome ? AF: 0.588 AC: 89388AN: 152068Hom.: 26971 Cov.: 32 AF XY: 0.593 AC XY: 44100AN XY: 74344
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Spinocerebellar ataxia type 42 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 14, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 14, 2021 | - - |
Spinocerebellar ataxia 42, early-onset, severe, with neurodevelopmental deficits Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 14, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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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