3-53810046-G-C
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001128840.3(CACNA1D):c.5940G>C(p.Ser1980Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000793 in 1,613,758 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 (★★).
Frequency
Consequence
NM_001128840.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CACNA1D | NM_000720.4 | c.6000G>C | p.Ser2000Ser | synonymous_variant | Exon 48 of 49 | ENST00000288139.11 | NP_000711.1 | |
CACNA1D | NM_001128840.3 | c.5940G>C | p.Ser1980Ser | 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.6000G>C | p.Ser2000Ser | synonymous_variant | Exon 48 of 49 | 1 | NM_000720.4 | ENSP00000288139.3 | ||
CACNA1D | ENST00000350061.11 | c.5940G>C | p.Ser1980Ser | synonymous_variant | Exon 47 of 48 | 1 | NM_001128840.3 | ENSP00000288133.5 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152078Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000175 AC: 44AN: 250892Hom.: 0 AF XY: 0.000273 AC XY: 37AN XY: 135642
GnomAD4 exome AF: 0.0000828 AC: 121AN: 1461680Hom.: 4 Cov.: 31 AF XY: 0.000128 AC XY: 93AN XY: 727140
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152078Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74274
ClinVar
Submissions by phenotype
not specified Benign:1
p.Ser2000Ser in exon 48 of CACNA1D: This variant is not expected to have clinica l significance because it does not alter an amino acid residue and is not locate d within the splice consensus sequence. It has been identified in 0.1% (30/30782 ) of South Asian chromosomes by the Genome Aggregation Database (gnomAD, http:// gnomad.broadinstitute.org; dbSNP rs767458712). -
Aldosterone-producing adenoma with seizures and neurological abnormalities Benign:1
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not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at