chr12-2115272-A-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP2BP4BP6BS2
The NM_000719.7(CACNA1C):āc.98A>Gā(p.Asn33Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000578 in 1,591,964 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N33T) has been classified as Uncertain significance.
Frequency
Consequence
NM_000719.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CACNA1C | NM_000719.7 | c.98A>G | p.Asn33Ser | missense_variant | 2/47 | ENST00000399655.6 | |
CACNA1C | NM_001167623.2 | c.98A>G | p.Asn33Ser | missense_variant | 2/47 | ENST00000399603.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CACNA1C | ENST00000399603.6 | c.98A>G | p.Asn33Ser | missense_variant | 2/47 | 5 | NM_001167623.2 | ||
CACNA1C | ENST00000399655.6 | c.98A>G | p.Asn33Ser | missense_variant | 2/47 | 1 | NM_000719.7 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152266Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000186 AC: 4AN: 215566Hom.: 0 AF XY: 0.0000255 AC XY: 3AN XY: 117426
GnomAD4 exome AF: 0.0000625 AC: 90AN: 1439698Hom.: 0 Cov.: 32 AF XY: 0.0000546 AC XY: 39AN XY: 713716
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152266Hom.: 0 Cov.: 34 AF XY: 0.0000269 AC XY: 2AN XY: 74402
ClinVar
Submissions by phenotype
Timothy syndrome;C2678478:Brugada syndrome 3 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 31, 2018 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Apr 02, 2020 | Has not been previously published as pathogenic or benign to our knowledge; Reported in ClinVar as a variant of uncertain significance (ClinVar Variant ID# 190679; Landrum et al., 2016); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function - |
Long QT syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 30, 2023 | - - |
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | May 18, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at