chr3-53810217-A-G
Variant summary
Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_000720.4(CACNA1D):c.6171A>G(p.Thr2057Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00135 in 1,613,860 control chromosomes in the GnomAD database, including 29 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as 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 -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CACNA1D | NM_000720.4 | c.6171A>G | p.Thr2057Thr | synonymous_variant | Exon 48 of 49 | ENST00000288139.11 | NP_000711.1 | |
CACNA1D | NM_001128840.3 | c.6111A>G | p.Thr2037Thr | synonymous_variant | Exon 47 of 48 | ENST00000350061.11 | NP_001122312.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CACNA1D | ENST00000288139.11 | c.6171A>G | p.Thr2057Thr | synonymous_variant | Exon 48 of 49 | 1 | NM_000720.4 | ENSP00000288139.3 | ||
CACNA1D | ENST00000350061.11 | c.6111A>G | p.Thr2037Thr | synonymous_variant | Exon 47 of 48 | 1 | NM_001128840.3 | ENSP00000288133.5 |
Frequencies
GnomAD3 genomes AF: 0.00700 AC: 1065AN: 152128Hom.: 16 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.00200 AC: 502AN: 251024 AF XY: 0.00148 show subpopulations
GnomAD4 exome AF: 0.000754 AC: 1102AN: 1461614Hom.: 13 Cov.: 31 AF XY: 0.000653 AC XY: 475AN XY: 727120 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.00702 AC: 1069AN: 152246Hom.: 16 Cov.: 32 AF XY: 0.00682 AC XY: 508AN XY: 74456 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
not specified Benign:2
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Thr2057Thr in exon 48 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 2.1% (94/4406) o f African American chromosomes from a broad population by the NHLBI Exome Sequen cing Project (http://evs.gs.washington.edu/EVS; dbSNP rs76868547). -
not provided Benign:2
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at