3-53495213-A-G
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 1P and 2B. PP2BP4_Moderate
The NM_000720.4(CACNA1D):c.47A>G(p.Gln16Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000062 in 1,613,732 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_000720.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CACNA1D | NM_000720.4 | c.47A>G | p.Gln16Arg | missense_variant | 1/49 | ENST00000288139.11 | |
CACNA1D | NM_001128840.3 | c.47A>G | p.Gln16Arg | missense_variant | 1/48 | ENST00000350061.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CACNA1D | ENST00000288139.11 | c.47A>G | p.Gln16Arg | missense_variant | 1/49 | 1 | NM_000720.4 | P2 | |
CACNA1D | ENST00000350061.11 | c.47A>G | p.Gln16Arg | missense_variant | 1/48 | 1 | NM_001128840.3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152162Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000161 AC: 4AN: 248688Hom.: 0 AF XY: 0.0000223 AC XY: 3AN XY: 134760
GnomAD4 exome AF: 0.00000411 AC: 6AN: 1461570Hom.: 0 Cov.: 34 AF XY: 0.00000688 AC XY: 5AN XY: 727078
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152162Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74332
ClinVar
Submissions by phenotype
not provided Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Mar 08, 2022 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). ClinVar contains an entry for this variant (Variation ID: 1305302). This variant has not been reported in the literature in individuals affected with CACNA1D-related conditions. This variant is present in population databases (rs760088044, gnomAD 0.007%). This sequence change replaces glutamine, which is neutral and polar, with arginine, which is basic and polar, at codon 16 of the CACNA1D protein (p.Gln16Arg). - |
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Apr 25, 2019 | Has not been previously published as pathogenic or benign to our knowledge - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at