NM_000720.4:c.1809C>T
Variant summary
Our verdict is Benign. The variant received -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS1
The NM_000720.4(CACNA1D):c.1809C>T(p.Phe603Phe) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000527 in 1,614,048 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 (★★).
Frequency
Consequence
NM_000720.4 synonymous
Scores
Clinical Significance
Conservation
Publications
- aldosterone-producing adenoma with seizures and neurological abnormalitiesInheritance: AD Classification: DEFINITIVE, STRONG, MODERATE Submitted by: Illumina, Ambry Genetics, Labcorp Genetics (formerly Invitae), G2P
- sinoatrial node dysfunction and deafnessInheritance: AR Classification: STRONG, MODERATE, SUPPORTIVE Submitted by: PanelApp Australia, Orphanet, G2P, ClinGen, Labcorp Genetics (formerly Invitae)
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ACMG classification
Our verdict: Benign. The variant received -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CACNA1D | NM_000720.4 | c.1809C>T | p.Phe603Phe | synonymous_variant | Exon 14 of 49 | ENST00000288139.11 | NP_000711.1 | |
CACNA1D | NM_001128840.3 | c.1749C>T | p.Phe583Phe | synonymous_variant | Exon 13 of 48 | ENST00000350061.11 | NP_001122312.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CACNA1D | ENST00000288139.11 | c.1809C>T | p.Phe603Phe | synonymous_variant | Exon 14 of 49 | 1 | NM_000720.4 | ENSP00000288139.3 | ||
CACNA1D | ENST00000350061.11 | c.1749C>T | p.Phe583Phe | synonymous_variant | Exon 13 of 48 | 1 | NM_001128840.3 | ENSP00000288133.5 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152070Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.0000477 AC: 12AN: 251494 AF XY: 0.0000589 show subpopulations
GnomAD4 exome AF: 0.0000506 AC: 74AN: 1461860Hom.: 0 Cov.: 32 AF XY: 0.0000578 AC XY: 42AN XY: 727238 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152188Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74420 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
not specified Benign:1
p.Phe603Phe in exon 14 of CACNA1D: This variant is not expected to have clinical significance because it does not alter an amino acid residue and it is not loca ted within the splice consensus sequence. It has been identified in 7/121412 of the total chromosomes across several populations by the Exome Aggregation Conso rtium (ExAC, http://exac.broadinstitute.org; dbSNP rs565265907). -
not provided Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at