rs535291848
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 1P and 13B. PP2BP4BP6_Very_StrongBS2
The ENST00000399655.6(CACNA1C):c.6026G>A(p.Arg2009Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000167 in 1,612,584 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 Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R2009W) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000399655.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CACNA1C | NM_000719.7 | c.6026G>A | p.Arg2009Gln | missense_variant | 46/47 | ENST00000399655.6 | NP_000710.5 | |
CACNA1C | NM_001167623.2 | c.6026G>A | p.Arg2009Gln | missense_variant | 46/47 | ENST00000399603.6 | NP_001161095.1 | |
CACNA1C-AS1 | NR_045725.1 | n.333+1452C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CACNA1C | ENST00000399603.6 | c.6026G>A | p.Arg2009Gln | missense_variant | 46/47 | 5 | NM_001167623.2 | ENSP00000382512 | ||
CACNA1C | ENST00000399655.6 | c.6026G>A | p.Arg2009Gln | missense_variant | 46/47 | 1 | NM_000719.7 | ENSP00000382563 | ||
CACNA1C-AS1 | ENST00000501371.5 | n.294+1452C>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152166Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000287 AC: 7AN: 244034Hom.: 0 AF XY: 0.0000376 AC XY: 5AN XY: 132992
GnomAD4 exome AF: 0.0000158 AC: 23AN: 1460300Hom.: 0 Cov.: 33 AF XY: 0.0000179 AC XY: 13AN XY: 726474
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152284Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74488
ClinVar
Submissions by phenotype
Long QT syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Aug 30, 2023 | - - |
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 11, 2022 | 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