chr3-53808713-G-A
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6_Very_StrongBP7
The NM_000720.4(CACNA1D):c.5874G>A(p.Pro1958=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000211 in 1,609,172 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. P1958P) has been classified as Likely benign.
Frequency
Consequence
NM_000720.4 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CACNA1D | NM_000720.4 | c.5874G>A | p.Pro1958= | synonymous_variant | 47/49 | ENST00000288139.11 | |
CACNA1D | NM_001128840.3 | c.5814G>A | p.Pro1938= | synonymous_variant | 46/48 | ENST00000350061.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CACNA1D | ENST00000288139.11 | c.5874G>A | p.Pro1958= | synonymous_variant | 47/49 | 1 | NM_000720.4 | P2 | |
CACNA1D | ENST00000350061.11 | c.5814G>A | p.Pro1938= | synonymous_variant | 46/48 | 1 | NM_001128840.3 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152122Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000485 AC: 12AN: 247656Hom.: 0 AF XY: 0.0000298 AC XY: 4AN XY: 134258
GnomAD4 exome AF: 0.0000199 AC: 29AN: 1456932Hom.: 0 Cov.: 31 AF XY: 0.0000166 AC XY: 12AN XY: 725038
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152240Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74430
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 14, 2017 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Mar 26, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at