rs150463212
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_000720.4(CACNA1D):c.5037G>A(p.Ser1679=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000308 in 1,614,084 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. S1679S) has been classified as Likely benign.
Frequency
Consequence
NM_000720.4 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CACNA1D | NM_000720.4 | c.5037G>A | p.Ser1679= | synonymous_variant | 42/49 | ENST00000288139.11 | |
CACNA1D | NM_001128840.3 | c.4977G>A | p.Ser1659= | synonymous_variant | 41/48 | ENST00000350061.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CACNA1D | ENST00000288139.11 | c.5037G>A | p.Ser1679= | synonymous_variant | 42/49 | 1 | NM_000720.4 | P2 | |
CACNA1D | ENST00000350061.11 | c.4977G>A | p.Ser1659= | synonymous_variant | 41/48 | 1 | NM_001128840.3 |
Frequencies
GnomAD3 genomes AF: 0.000368 AC: 56AN: 152220Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000561 AC: 141AN: 251494Hom.: 1 AF XY: 0.000471 AC XY: 64AN XY: 135920
GnomAD4 exome AF: 0.000302 AC: 441AN: 1461746Hom.: 4 Cov.: 30 AF XY: 0.000297 AC XY: 216AN XY: 727182
GnomAD4 genome AF: 0.000368 AC: 56AN: 152338Hom.: 0 Cov.: 32 AF XY: 0.000215 AC XY: 16AN XY: 74494
ClinVar
Submissions by phenotype
not specified Benign:3
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | May 01, 2020 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 05, 2017 | 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. - |
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Nov 24, 2014 | Ser1679Ser in exon 42 of CACNA1D: This variant is not expected to have clinical significance because it does not alter an amino acid residue and is not located within the splice consensus sequence. It has been identified in 0.1% (6/8600) of European American chromosomes from a broad population by the NHLBI Exome Sequen cing Project (http://evs.gs.washington.edu/EVS; dbSNP rs150463212). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 16, 2024 | - - |
CACNA1D-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 01, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at