rs776275799
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 1P and 8B. PP2BP4_ModerateBP6_ModerateBS2
The NM_000719.7(CACNA1C):c.6254G>A(p.Gly2085Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000413 in 1,451,220 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/18 in silico tools predict 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. G2085S) has been classified as Uncertain significance.
Frequency
Consequence
NM_000719.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CACNA1C | NM_000719.7 | c.6254G>A | p.Gly2085Asp | missense_variant | 47/47 | ENST00000399655.6 | |
CACNA1C | NM_001167623.2 | c.6254G>A | p.Gly2085Asp | missense_variant | 47/47 | ENST00000399603.6 | |
CACNA1C-AS1 | NR_045725.1 | n.89+33C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CACNA1C | ENST00000399603.6 | c.6254G>A | p.Gly2085Asp | missense_variant | 47/47 | 5 | NM_001167623.2 | ||
CACNA1C | ENST00000399655.6 | c.6254G>A | p.Gly2085Asp | missense_variant | 47/47 | 1 | NM_000719.7 | ||
CACNA1C-AS1 | ENST00000501371.5 | n.50+33C>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 152182Hom.: 0 Cov.: 33 FAILED QC
GnomAD3 exomes AF: 0.0000133 AC: 3AN: 225142Hom.: 0 AF XY: 0.00000815 AC XY: 1AN XY: 122750
GnomAD4 exome AF: 0.00000413 AC: 6AN: 1451220Hom.: 0 Cov.: 31 AF XY: 0.00000416 AC XY: 3AN XY: 720984
GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 152182Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74340
ClinVar
Submissions by phenotype
Long QT syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 17, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at