rs767458712
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS1
The NM_000720.4(CACNA1D):c.6000G>A(p.Ser2000=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000341 in 1,613,758 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 (★). Synonymous variant affecting the same amino acid position (i.e. S2000S) has been classified as Likely benign.
Frequency
Consequence
NM_000720.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CACNA1D | NM_000720.4 | c.6000G>A | p.Ser2000= | synonymous_variant | 48/49 | ENST00000288139.11 | |
CACNA1D | NM_001128840.3 | c.5940G>A | p.Ser1980= | synonymous_variant | 47/48 | ENST00000350061.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CACNA1D | ENST00000288139.11 | c.6000G>A | p.Ser2000= | synonymous_variant | 48/49 | 1 | NM_000720.4 | P2 | |
CACNA1D | ENST00000350061.11 | c.5940G>A | p.Ser1980= | synonymous_variant | 47/48 | 1 | NM_001128840.3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 152078Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000124 AC: 31AN: 250892Hom.: 0 AF XY: 0.000118 AC XY: 16AN XY: 135642
GnomAD4 exome AF: 0.0000363 AC: 53AN: 1461680Hom.: 0 Cov.: 31 AF XY: 0.0000371 AC XY: 27AN XY: 727140
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 152078Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74274
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 01, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at